From ed7800657b800724445906c9151582c4791c92ad Mon Sep 17 00:00:00 2001 From: mjt320 Date: Mon, 29 Aug 2022 15:37:44 +0100 Subject: [PATCH 1/9] naming --- .gitignore | 2 +- ...loU_Norway.py => test_DCEmodels_2CXM_OGJ_OsloU_NOR.py} | 4 ++-- ...U_Norway.py => test_DCEmodels_etofts_OGJ_OsloU_NOR.py} | 6 ++++-- ... => test_DCEmodels_etofts_OG_MO_AUMC_ICR_RMH_ND_UK.py} | 5 +++-- ...fts_LCB_BNI.py => test_DCEmodels_tofts_LCB_BNI_USA.py} | 3 ++- ...oU_Norway.py => test_DCEmodels_tofts_OGJ_OsloU_NOR.py} | 6 ++++-- ...ST_SydneyAus.py => test_popAIF_Parker_ST_SydneyAUS.py} | 3 ++- ...dneyAus.py => test_popAIF_preclinical_ST_SydneyAUS.py} | 3 ++- ...est_SI2Conc_LCB_BNI.py => test_SI2Conc_LCB_BNI_USA.py} | 3 ++- ...CR_RMH.py => test_SI2Conc_OG_MO_AUMC_ICR_RMH_ND_UK.py} | 3 ++- ...UMC_ICR_RMH.py => test_t1_OG_MO_AUMC_ICR_RMH_ND_UK.py} | 6 ++++-- .../{test_t1_ST_SydneyAus.py => test_t1_ST_SydneyAUS.py} | 8 ++++---- .../{test_t1_McGill_Can.py => test_t1_ZA_McGill_CAN.py} | 6 ++++-- 13 files changed, 36 insertions(+), 22 deletions(-) rename test/DCEmodels/{test_DCEmodels_2CXM_OGJ_OsloU_Norway.py => test_DCEmodels_2CXM_OGJ_OsloU_NOR.py} (94%) rename test/DCEmodels/{test_DCEmodels_etofts_OGJ_OsloU_Norway.py => test_DCEmodels_etofts_OGJ_OsloU_NOR.py} (91%) rename test/DCEmodels/{test_DCEmodels_etofts_OG_MO_AUMC_ICR_RMH.py => test_DCEmodels_etofts_OG_MO_AUMC_ICR_RMH_ND_UK.py} (95%) rename test/DCEmodels/{test_DCEmodels_tofts_LCB_BNI.py => test_DCEmodels_tofts_LCB_BNI_USA.py} (92%) rename test/DCEmodels/{test_DCEmodels_tofts_OGJ_OsloU_Norway.py => test_DCEmodels_tofts_OGJ_OsloU_NOR.py} (91%) rename test/PopulationAIF_DCE/{test_popAIF_Parker_ST_SydneyAus.py => test_popAIF_Parker_ST_SydneyAUS.py} (94%) rename test/PopulationAIF_DCE/{test_popAIF_preclinical_ST_SydneyAus.py => test_popAIF_preclinical_ST_SydneyAUS.py} (93%) rename test/SI_to_Conc/{test_SI2Conc_LCB_BNI.py => test_SI2Conc_LCB_BNI_USA.py} (92%) rename test/SI_to_Conc/{test_SI2Conc_OG_MO_AUMC_ICR_RMH.py => test_SI2Conc_OG_MO_AUMC_ICR_RMH_ND_UK.py} (93%) rename test/T1_mapping/{test_t1_OG_MO_AUMC_ICR_RMH.py => test_t1_OG_MO_AUMC_ICR_RMH_ND_UK.py} (90%) rename test/T1_mapping/{test_t1_ST_SydneyAus.py => test_t1_ST_SydneyAUS.py} (91%) rename test/T1_mapping/{test_t1_McGill_Can.py => test_t1_ZA_McGill_CAN.py} (89%) diff --git a/.gitignore b/.gitignore index 1a6ef752..20c7a436 100644 --- a/.gitignore +++ b/.gitignore @@ -162,4 +162,4 @@ notebooks/_build # Misc .DS_Store - +.pylint.d diff --git a/test/DCEmodels/test_DCEmodels_2CXM_OGJ_OsloU_Norway.py b/test/DCEmodels/test_DCEmodels_2CXM_OGJ_OsloU_NOR.py similarity index 94% rename from test/DCEmodels/test_DCEmodels_2CXM_OGJ_OsloU_Norway.py rename to test/DCEmodels/test_DCEmodels_2CXM_OGJ_OsloU_NOR.py index f75cfd9f..baa7aa9d 100644 --- a/test/DCEmodels/test_DCEmodels_2CXM_OGJ_OsloU_Norway.py +++ b/test/DCEmodels/test_DCEmodels_2CXM_OGJ_OsloU_NOR.py @@ -3,7 +3,7 @@ from time import perf_counter from ..helpers import osipi_parametrize, log_init, log_results from . import DCEmodels_data -from src.original.OGJ_OsloU_Norway.MRImageAnalysis.DCE.Analyze import fitToModel +from src.original.OGJ_OsloU_NOR.MRImageAnalysis.DCE.Analyze import fitToModel arg_names = 'label, t_array, C_t_array, cp_aif_array, vp_ref, ve_ref, fp_ref,' \ 'ps_ref, delay_ref, a_tol_vp, r_tol_vp, a_tol_ve, r_tol_ve, ' \ @@ -25,7 +25,7 @@ def setup_module(module): # Use the test data to generate a parametrize decorator. This causes the following # test to be run for every test case listed in test_data... @osipi_parametrize(arg_names, test_data, xf_labels=[]) -def test_OGJ_OsloU_Norway_2cxm_model_llsq(label, t_array, C_t_array, +def test_OGJ_OsloU_NOR_2cxm_model_llsq(label, t_array, C_t_array, cp_aif_array, vp_ref, ve_ref, fp_ref, ps_ref, delay_ref, a_tol_vp, r_tol_vp, a_tol_ve, diff --git a/test/DCEmodels/test_DCEmodels_etofts_OGJ_OsloU_Norway.py b/test/DCEmodels/test_DCEmodels_etofts_OGJ_OsloU_NOR.py similarity index 91% rename from test/DCEmodels/test_DCEmodels_etofts_OGJ_OsloU_Norway.py rename to test/DCEmodels/test_DCEmodels_etofts_OGJ_OsloU_NOR.py index f07e65f3..76f7567c 100644 --- a/test/DCEmodels/test_DCEmodels_etofts_OGJ_OsloU_Norway.py +++ b/test/DCEmodels/test_DCEmodels_etofts_OGJ_OsloU_NOR.py @@ -24,7 +24,8 @@ def setup_module(module): # Use the test data to generate a parametrize decorator. This causes the following test to be run for every test case # listed in test_data... @osipi_parametrize(arg_names, test_data, xf_labels=[]) -def test_OGJ_OsloU_Norway_extended_tofts_kety_model_llsq(label, t_array, C_array, ca_array, ta_array, ve_ref, vp_ref, +def test_OGJ_OsloU_NOR_extended_tofts_kety_model_llsq(label, t_array, C_array, + ca_array, ta_array, ve_ref, vp_ref, Ktrans_ref, arterial_delay_ref, a_tol_ve, r_tol_ve, a_tol_vp, r_tol_vp, a_tol_Ktrans, r_tol_Ktrans, a_tol_delay, r_tol_delay): # NOTES: @@ -53,7 +54,8 @@ def test_OGJ_OsloU_Norway_extended_tofts_kety_model_llsq(label, t_array, C_array @osipi_parametrize(arg_names, test_data, xf_labels=[]) -def test_OGJ_OsloU_Norway_extended_tofts_kety_model_nlls(label, t_array, C_array, ca_array, ta_array, ve_ref, vp_ref, +def test_OGJ_OsloU_NOR_extended_tofts_kety_model_nlls(label, t_array, C_array, + ca_array, ta_array, ve_ref, vp_ref, Ktrans_ref, arterial_delay_ref, a_tol_ve, r_tol_ve, a_tol_vp, r_tol_vp, a_tol_Ktrans, r_tol_Ktrans, a_tol_delay, r_tol_delay): # NOTES: diff --git a/test/DCEmodels/test_DCEmodels_etofts_OG_MO_AUMC_ICR_RMH.py b/test/DCEmodels/test_DCEmodels_etofts_OG_MO_AUMC_ICR_RMH_ND_UK.py similarity index 95% rename from test/DCEmodels/test_DCEmodels_etofts_OG_MO_AUMC_ICR_RMH.py rename to test/DCEmodels/test_DCEmodels_etofts_OG_MO_AUMC_ICR_RMH_ND_UK.py index 35882c79..6ae5a13b 100644 --- a/test/DCEmodels/test_DCEmodels_etofts_OG_MO_AUMC_ICR_RMH.py +++ b/test/DCEmodels/test_DCEmodels_etofts_OG_MO_AUMC_ICR_RMH_ND_UK.py @@ -25,7 +25,8 @@ def setup_module(module): # Use the test data to generate a parametrize decorator. This causes the following # test to be run for every test case listed in test_data... @osipi_parametrize(arg_names, test_data, xf_labels=[]) -def testOG_MO_AUMC_ICR_RMH_extended_tofts_kety_model(label, t_array, C_array, ca_array, ta_array, ve_ref, vp_ref, +def test_OG_MO_AUMC_ICR_RMH_ND_UK_extended_tofts_kety_model(label, t_array, + C_array, ca_array, ta_array, ve_ref, vp_ref, Ktrans_ref, arterial_delay_ref, a_tol_ve, r_tol_ve, a_tol_vp, r_tol_vp, a_tol_Ktrans, r_tol_Ktrans, a_tol_delay, r_tol_delay): # NOTES: @@ -73,7 +74,7 @@ def testOG_MO_AUMC_ICR_RMH_extended_tofts_kety_model(label, t_array, C_array, ca # Use the test data to generate a parametrize decorator. This causes the following # test to be run for every test case listed in test_data... @osipi_parametrize(arg_names, test_data_delay, xf_labels=[]) -def testOG_MO_AUMC_ICR_RMH_extended_tofts_kety_model_delay(label, t_array, +def testOG_MO_AUMC_ICR_RMH_ND_UK_extended_tofts_kety_model_delay(label, t_array, C_array, ca_array, ta_array, ve_ref, vp_ref, Ktrans_ref, arterial_delay_ref, a_tol_ve, r_tol_ve, a_tol_vp, r_tol_vp, a_tol_Ktrans, r_tol_Ktrans, a_tol_delay, r_tol_delay): diff --git a/test/DCEmodels/test_DCEmodels_tofts_LCB_BNI.py b/test/DCEmodels/test_DCEmodels_tofts_LCB_BNI_USA.py similarity index 92% rename from test/DCEmodels/test_DCEmodels_tofts_LCB_BNI.py rename to test/DCEmodels/test_DCEmodels_tofts_LCB_BNI_USA.py index 2683c178..7bf98ec9 100644 --- a/test/DCEmodels/test_DCEmodels_tofts_LCB_BNI.py +++ b/test/DCEmodels/test_DCEmodels_tofts_LCB_BNI_USA.py @@ -23,7 +23,8 @@ def setup_module(module): # Use the test data to generate a parametrize decorator. This causes the following test to be run for every test case # listed in test_data... @osipi_parametrize(arg_names, test_data, xf_labels=[]) -def test_LCB_BNI_tofts_model(label, t_array, C_array, ca_array, ta_array, ve_ref, Ktrans_ref, arterial_delay_ref, +def test_LCB_BNI_USA_tofts_model(label, t_array, C_array, ca_array, ta_array, + ve_ref, Ktrans_ref, arterial_delay_ref, a_tol_ve, r_tol_ve, a_tol_Ktrans, r_tol_Ktrans, a_tol_delay, r_tol_delay): # NOTES: # Artery-capillary delay not implemented diff --git a/test/DCEmodels/test_DCEmodels_tofts_OGJ_OsloU_Norway.py b/test/DCEmodels/test_DCEmodels_tofts_OGJ_OsloU_NOR.py similarity index 91% rename from test/DCEmodels/test_DCEmodels_tofts_OGJ_OsloU_Norway.py rename to test/DCEmodels/test_DCEmodels_tofts_OGJ_OsloU_NOR.py index 42a51250..5b44b689 100644 --- a/test/DCEmodels/test_DCEmodels_tofts_OGJ_OsloU_Norway.py +++ b/test/DCEmodels/test_DCEmodels_tofts_OGJ_OsloU_NOR.py @@ -24,7 +24,8 @@ def setup_module(module): # Use the test data to generate a parametrize decorator. This causes the following test to be run for every test case # listed in test_data... @osipi_parametrize(arg_names, test_data, xf_labels=[]) -def test_OGJ_OsloU_Norway_tofts_model_llsq(label, t_array, C_array, ca_array, ta_array, ve_ref, Ktrans_ref, +def test_OGJ_OsloU_NOR_tofts_model_llsq(label, t_array, C_array, ca_array, + ta_array, ve_ref, Ktrans_ref, arterial_delay_ref, a_tol_ve, r_tol_ve, a_tol_Ktrans, r_tol_Ktrans, a_tol_delay, r_tol_delay): # NOTES: @@ -50,7 +51,8 @@ def test_OGJ_OsloU_Norway_tofts_model_llsq(label, t_array, C_array, ca_array, ta @osipi_parametrize(arg_names, test_data, xf_labels=[]) -def test_OGJ_OsloU_Norway_tofts_model_nlls(label, t_array, C_array, ca_array, ta_array, ve_ref, Ktrans_ref, +def test_OGJ_OsloU_NOR_tofts_model_nlls(label, t_array, C_array, ca_array, + ta_array, ve_ref, Ktrans_ref, arterial_delay_ref, a_tol_ve, r_tol_ve, a_tol_Ktrans, r_tol_Ktrans, a_tol_delay, r_tol_delay): # NOTES: diff --git a/test/PopulationAIF_DCE/test_popAIF_Parker_ST_SydneyAus.py b/test/PopulationAIF_DCE/test_popAIF_Parker_ST_SydneyAUS.py similarity index 94% rename from test/PopulationAIF_DCE/test_popAIF_Parker_ST_SydneyAus.py rename to test/PopulationAIF_DCE/test_popAIF_Parker_ST_SydneyAUS.py index 1e56e752..b101c9ca 100644 --- a/test/PopulationAIF_DCE/test_popAIF_Parker_ST_SydneyAus.py +++ b/test/PopulationAIF_DCE/test_popAIF_Parker_ST_SydneyAUS.py @@ -26,7 +26,8 @@ def setup_module(module): # test to be run for every test case listed in test_data. # some test data fails as this code uses a shift of the original AIF in time and doesn't recalculate the values based on the new time array @osipi_parametrize(arg_names, test_data, xf_labels=['delay_5.0s','delay_10.0s','delay_31.0s','delay_2.0s']) -def test_Parker_AIF_ST_SydneyAus(label, time, cb_ref_values, delay, a_tol, r_tol): +def test_Parker_AIF_ST_SydneyAUS(label, time, cb_ref_values, delay, a_tol, + r_tol): # prepare input data time = time*60 # time array is expected in seconds diff --git a/test/PopulationAIF_DCE/test_popAIF_preclinical_ST_SydneyAus.py b/test/PopulationAIF_DCE/test_popAIF_preclinical_ST_SydneyAUS.py similarity index 93% rename from test/PopulationAIF_DCE/test_popAIF_preclinical_ST_SydneyAus.py rename to test/PopulationAIF_DCE/test_popAIF_preclinical_ST_SydneyAUS.py index c9c74901..b1f8031c 100644 --- a/test/PopulationAIF_DCE/test_popAIF_preclinical_ST_SydneyAus.py +++ b/test/PopulationAIF_DCE/test_popAIF_preclinical_ST_SydneyAUS.py @@ -25,7 +25,8 @@ def setup_module(module): # Use the test data to generate a parametrize decorator. This causes the following # test to be run for every test case listed in test_data... @osipi_parametrize(arg_names, test_data, xf_labels=[]) -def test_preclinical_AIF_ST_SydneyAus(label, time, cb_ref_values, delay, a_tol, r_tol): +def test_preclinical_AIF_ST_SydneyAUS(label, time, cb_ref_values, delay, + a_tol, r_tol): # prepare input data t0 = delay + time[1] # precontrast signal; t0 is expected to be in seconds; if no precontrast signal is expected, the value should be equal to the temp resolution diff --git a/test/SI_to_Conc/test_SI2Conc_LCB_BNI.py b/test/SI_to_Conc/test_SI2Conc_LCB_BNI_USA.py similarity index 92% rename from test/SI_to_Conc/test_SI2Conc_LCB_BNI.py rename to test/SI_to_Conc/test_SI2Conc_LCB_BNI_USA.py index 1783245b..708ecb21 100644 --- a/test/SI_to_Conc/test_SI2Conc_LCB_BNI.py +++ b/test/SI_to_Conc/test_SI2Conc_LCB_BNI_USA.py @@ -24,7 +24,8 @@ def setup_module(module): # Use the test data to generate a parametrize decorator. This causes the following # test to be run for every test case listed in test_data... @osipi_parametrize(arg_names, test_data, xf_labels = []) -def test_LCB_BNI_sig_to_conc(label, fa, tr, T1base, BLpts, r1, s_array, conc_array, a_tol, r_tol): +def test_LCB_BNI_USA_SI2Conc(label, fa, tr, T1base, BLpts, r1, + s_array, conc_array, a_tol, r_tol): # Note: the first signal value is not used for baseline estimation, # and the first C value is not logged or assessed diff --git a/test/SI_to_Conc/test_SI2Conc_OG_MO_AUMC_ICR_RMH.py b/test/SI_to_Conc/test_SI2Conc_OG_MO_AUMC_ICR_RMH_ND_UK.py similarity index 93% rename from test/SI_to_Conc/test_SI2Conc_OG_MO_AUMC_ICR_RMH.py rename to test/SI_to_Conc/test_SI2Conc_OG_MO_AUMC_ICR_RMH_ND_UK.py index a8ae170c..2bfe5100 100644 --- a/test/SI_to_Conc/test_SI2Conc_OG_MO_AUMC_ICR_RMH.py +++ b/test/SI_to_Conc/test_SI2Conc_OG_MO_AUMC_ICR_RMH_ND_UK.py @@ -26,7 +26,8 @@ def setup_module(module): # Use the test data to generate a parametrize decorator. This causes the following # test to be run for every test case listed in test_data... @osipi_parametrize(arg_names, test_data, xf_labels = []) -def test_OG_MO_AUMC_ICR_RMH_dce_to_r1eff(label, fa, tr, T1base, BLpts, r1, s_array, conc_array, a_tol, r_tol): +def test_OG_MO_AUMC_ICR_RMH_ND_UK_SI2Conc(label, fa, tr, T1base, + BLpts, r1, s_array, conc_array, a_tol, r_tol): # Note: the first signal value is not used for baseline estimation, # and the first C value is not logged or assessed diff --git a/test/T1_mapping/test_t1_OG_MO_AUMC_ICR_RMH.py b/test/T1_mapping/test_t1_OG_MO_AUMC_ICR_RMH_ND_UK.py similarity index 90% rename from test/T1_mapping/test_t1_OG_MO_AUMC_ICR_RMH.py rename to test/T1_mapping/test_t1_OG_MO_AUMC_ICR_RMH_ND_UK.py index 8e66d315..d6c91cb2 100644 --- a/test/T1_mapping/test_t1_OG_MO_AUMC_ICR_RMH.py +++ b/test/T1_mapping/test_t1_OG_MO_AUMC_ICR_RMH_ND_UK.py @@ -30,7 +30,8 @@ def setup_module(module): # test to be run for every test case listed in test_data... # In the following test, we specify 1 case that is expected to fail... @osipi_parametrize(arg_names, test_data, xf_labels = ['Pat5_voxel5_prostaat']) -def testOG_MO_AUMC_ICR_RMH_t1_VFA_2fa(label, fa_array, tr_array, s_array, r1_ref, s0_ref, a_tol, r_tol): +def test_OG_MO_AUMC_ICR_RMH_ND_UK_t1_VFA_2fa(label, fa_array, tr_array, + s_array, r1_ref, s0_ref, a_tol, r_tol): # NOTES: # Code requires signal array with min 2 dimensions (including FA) # Expected fails: 1 low-SNR prostate voxel @@ -51,7 +52,8 @@ def testOG_MO_AUMC_ICR_RMH_t1_VFA_2fa(label, fa_array, tr_array, s_array, r1_ref @osipi_parametrize(arg_names, test_data, xf_labels=[]) -def testOG_MO_AUMC_ICR_RMH_t1_VFA(label, fa_array, tr_array, s_array, r1_ref, s0_ref, a_tol, r_tol): +def test_OG_MO_AUMC_ICR_RMH_ND_UK_t1_VFA(label, fa_array, tr_array, s_array, + r1_ref, s0_ref, a_tol, r_tol): # NOTES: # Code requires signal array with min 2 dimensions (including FA) # Expected fails: 1 low-SNR prostate voxel diff --git a/test/T1_mapping/test_t1_ST_SydneyAus.py b/test/T1_mapping/test_t1_ST_SydneyAUS.py similarity index 91% rename from test/T1_mapping/test_t1_ST_SydneyAus.py rename to test/T1_mapping/test_t1_ST_SydneyAUS.py index 557f0700..996ad8a3 100644 --- a/test/T1_mapping/test_t1_ST_SydneyAus.py +++ b/test/T1_mapping/test_t1_ST_SydneyAUS.py @@ -28,7 +28,8 @@ def setup_module(module): # Use the test data to generate a parametrize decorator. This causes the following # test to be run for every test case listed in test_data... @osipi_parametrize(arg_names, test_data, xf_labels = []) -def test_ST_SydneyAus_t1_VFA_nonlin(label, fa_array, tr_array, s_array, r1_ref, s0_ref, a_tol, r_tol): +def test_ST_SydneyAUS_t1_VFA_nonlin(label, fa_array, tr_array, s_array, + r1_ref, s0_ref, a_tol, r_tol): # NOTES: # prepare input data @@ -46,7 +47,8 @@ def test_ST_SydneyAus_t1_VFA_nonlin(label, fa_array, tr_array, s_array, r1_ref, # In the following test, we specify 1 case that is expected to fail... @osipi_parametrize(arg_names, test_data, xf_labels = ['Pat5_voxel5_prostaat']) -def test_ST_SydneyAus_t1_VFA_lin(label, fa_array, tr_array, s_array, r1_ref, s0_ref, a_tol, r_tol): +def test_ST_SydneyAUS_t1_VFA_lin(label, fa_array, tr_array, s_array, r1_ref, + s0_ref, a_tol, r_tol): # NOTES: # Signal is scaled to prevent multiple test failures for prostate test cases. # Linear mode uses linear model but not linear regression(?) @@ -64,5 +66,3 @@ def test_ST_SydneyAus_t1_VFA_lin(label, fa_array, tr_array, s_array, r1_ref, s0_ r1_lin_meas = 1000./t1_lin_meas # convert T1 (ms) to R1 (/s) log_results(filename_prefix, '_ST_SydneyAus_t1_VFA_lin', [[label, f"{exc_time:.0f}", r1_ref, r1_lin_meas]]) # log results to csv np.testing.assert_allclose([r1_lin_meas], [r1_ref], rtol=r_tol, atol=a_tol) - - diff --git a/test/T1_mapping/test_t1_McGill_Can.py b/test/T1_mapping/test_t1_ZA_McGill_CAN.py similarity index 89% rename from test/T1_mapping/test_t1_McGill_Can.py rename to test/T1_mapping/test_t1_ZA_McGill_CAN.py index 6f8c7151..0ca8f016 100644 --- a/test/T1_mapping/test_t1_McGill_Can.py +++ b/test/T1_mapping/test_t1_ZA_McGill_CAN.py @@ -28,7 +28,8 @@ def setup_module(module): # Use the test data to generate a parametrize decorator. This causes the following # test to be run for every test case listed in test_data... @osipi_parametrize(arg_names, test_data, xf_labels = []) -def test_mcgill_t1_novifast(label, fa_array, tr_array, s_array, r1_ref, s0_ref, a_tol, r_tol): +def test_ZA_McGill_CAN_t1_novifast(label, fa_array, tr_array, s_array, r1_ref, + s0_ref, a_tol, r_tol): # NOTES: # prepare input data @@ -48,7 +49,8 @@ def test_mcgill_t1_novifast(label, fa_array, tr_array, s_array, r1_ref, s0_ref, # In the following test, we specify 1 case that is expected to fail... @osipi_parametrize(arg_names, test_data, xf_labels = ['Pat5_voxel5_prostaat']) -def test_mcgill_t1_VFA_lin(label, fa_array, tr_array, s_array, r1_ref, s0_ref, a_tol, r_tol): +def test_ZA_McGill_CAN_t1_VFA_lin(label, fa_array, tr_array, s_array, + r1_ref, s0_ref, a_tol, r_tol): # NOTES: # Expected fails: 1 low-SNR prostate voxel From 024d17f999d26d6b21eb796247307eea1b8e2b3e Mon Sep 17 00:00:00 2001 From: mjt320 Date: Wed, 31 Aug 2022 13:51:33 +0100 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OGJ_OsloU_NOR}/MRImageAnalysis/Data/AIF_DCE/026/07/AIF_DCE.txt (100%) rename src/original/{OGJ_OsloU_Norway => OGJ_OsloU_NOR}/MRImageAnalysis/Data/AIF_DCE/027/01/AIF_DCE.txt (100%) rename src/original/{OGJ_OsloU_Norway => OGJ_OsloU_NOR}/MRImageAnalysis/Data/AIF_DCE/027/02/AIF_DCE.txt (100%) rename src/original/{OGJ_OsloU_Norway => OGJ_OsloU_NOR}/MRImageAnalysis/Data/AIF_DCE/027/03/AIF_DCE.txt (100%) rename src/original/{OGJ_OsloU_Norway => OGJ_OsloU_NOR}/MRImageAnalysis/Data/AIF_DCE/027/04/AIF_DCE.txt (100%) rename src/original/{OGJ_OsloU_Norway => OGJ_OsloU_NOR}/MRImageAnalysis/Data/AIF_DCE/027/06/AIF_DCE.txt (100%) rename src/original/{OGJ_OsloU_Norway => OGJ_OsloU_NOR}/MRImageAnalysis/Data/AIF_DCE/AIF_600.csv (100%) rename src/original/{OGJ_OsloU_Norway => OGJ_OsloU_NOR}/MRImageAnalysis/Data/Aorta.txt (100%) rename src/original/{OGJ_OsloU_Norway => OGJ_OsloU_NOR}/MRImageAnalysis/MRImage.py (100%) rename src/original/{OGJ_OsloU_Norway/MRImageAnalysis/DCE => OGJ_OsloU_NOR/MRImageAnalysis}/__init__.py (100%) rename src/original/{OGJ_OsloU_Norway => OGJ_OsloU_NOR}/MRImageAnalysis/io.py (100%) rename src/original/{OGJ_OsloU_Norway => OGJ_OsloU_NOR}/MRImageAnalysis/math.py (100%) rename src/original/{OGJ_OsloU_Norway => OGJ_OsloU_NOR}/Simulations/bat/optimal_BAT_and_range.py (100%) rename src/original/{OGJ_OsloU_Norway => OGJ_OsloU_NOR}/Simulations/bat/run.py (100%) rename src/original/{OGJ_OsloU_Norway => OGJ_OsloU_NOR}/Simulations/bir/imports.py (100%) rename src/original/{OGJ_OsloU_Norway => OGJ_OsloU_NOR}/Simulations/bir/run.py (100%) rename src/original/{OGJ_OsloU_Norway => OGJ_OsloU_NOR}/Simulations/frequency_analysis/imports.py (100%) rename src/original/{OGJ_OsloU_Norway => OGJ_OsloU_NOR}/Simulations/frequency_analysis/run.py (100%) rename src/original/{OGJ_OsloU_Norway => OGJ_OsloU_NOR}/Simulations/noise/run.py (100%) rename src/original/{OGJ_OsloU_Norway => OGJ_OsloU_NOR}/Simulations/sample_data/run.py (100%) rename src/original/{OGJ_OsloU_Norway => OGJ_OsloU_NOR}/Simulations/transfer_functions/imports.py (100%) rename src/original/{OGJ_OsloU_Norway => OGJ_OsloU_NOR}/Simulations/transfer_functions/run.py (100%) rename src/original/{OGJ_OsloU_Norway => OGJ_OsloU_NOR}/Thumbs.db (100%) rename src/original/{OGJ_OsloU_Norway/MRImageAnalysis => OGJ_OsloU_NOR}/__init__.py (100%) rename src/original/{OGJ_OsloU_Norway => OGJ_OsloU_NOR}/phantoms_json/nICE.json (100%) rename src/original/{OGJ_OsloU_Norway => OGJ_OsloU_NOR}/phantoms_json/phantom10.json (100%) rename src/original/{OGJ_OsloU_Norway => OGJ_OsloU_NOR}/phantoms_json/phantom11.json (100%) rename src/original/{OGJ_OsloU_Norway => OGJ_OsloU_NOR}/phantoms_json/phantom12.json (100%) rename src/original/{OGJ_OsloU_Norway => OGJ_OsloU_NOR}/phantoms_json/phantom13a.json (100%) rename src/original/{OGJ_OsloU_Norway => OGJ_OsloU_NOR}/phantoms_json/phantom13b.json (100%) rename src/original/{OGJ_OsloU_Norway => OGJ_OsloU_NOR}/phantoms_json/phantom13c.json (100%) rename src/original/{OGJ_OsloU_Norway => OGJ_OsloU_NOR}/phantoms_json/phantom8a.json (100%) rename src/original/{OGJ_OsloU_Norway => OGJ_OsloU_NOR}/phantoms_json/phantom8a_for_nICE.json (100%) rename src/original/{OGJ_OsloU_Norway => OGJ_OsloU_NOR}/phantoms_json/phantom9-noisy.json (100%) rename src/original/{OGJ_OsloU_Norway => OGJ_OsloU_NOR}/phantoms_json/phantom9.json (100%) rename src/original/{OGJ_OsloU_Norway => OGJ_OsloU_NOR}/phantoms_json/sample_data.json (100%) rename src/original/{OGJ_OsloU_Norway => OGJ_OsloU_NOR}/phantoms_json/sim_with_noise.json (100%) rename src/original/{OGJ_OsloU_Norway => OGJ_OsloU_NOR}/phantoms_py/phantom.py (100%) rename src/original/{OG_MO_AUMC_ICR_RMH => OG_MO_AUMC_ICR_RMH_NL_UK}/ExtendedTofts/DCE.py (100%) rename src/original/{OGJ_OsloU_Norway => OG_MO_AUMC_ICR_RMH_NL_UK/ExtendedTofts}/__init__.py (100%) rename src/original/{OG_MO_AUMC_ICR_RMH => OG_MO_AUMC_ICR_RMH_NL_UK}/ExtendedTofts/hpexample.py (100%) rename src/original/{OG_MO_AUMC_ICR_RMH => OG_MO_AUMC_ICR_RMH_NL_UK}/ExtendedTofts/sim_lsq.py (100%) rename src/original/{OG_MO_AUMC_ICR_RMH/ExtendedTofts => OG_MO_AUMC_ICR_RMH_NL_UK}/__init__.py (100%) rename src/original/{OG_MO_AUMC_ICR_RMH => ZA_McGill_CAN}/__init__.py (100%) rename src/original/{McGill_Can => ZA_McGill_CAN}/vfa.py (100%) diff --git a/.pylint.d/test.DCEmodels.test_LEK_UoEdinburghUK1.stats b/.pylint.d/test.DCEmodels.test_LEK_UoEdinburghUK1.stats deleted file mode 100644 index caecda559938486e9f793087a7f04eb11480e255..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 1075 zcmZWo%Wm5+5L9AYiSuk?1PyX-fL!E5f1wS6fW78e2oyi zPx_uq$edZ`PXr^8SXpXCA;31|%8w;1bVDM4#5BAhC^a-><`0cnP-eAh$i6>VQ3Dc| z4Vn6hFead}pDd`Q3c0TGad1;D+XSadf=H~^iPC{H@-u6wM0A;~a*5VT%0$pTk?=y5 zq zxC%*qhK5Z1d567FBWZ?H!=$GjCfgE1HJ2-cJxkU=f|3GTJ#u+WqWpl&@71k5^vyAf4>3(m5gB}`!KJ>`8+=e;Gp7e3l zTJ#ugNolBXxAy!XwW)dEU-Uc)VNdWWkcZGs%f|j=AKIErLn4_ui>-_N3_Gt`J3qm< z3cA|Cw`=%^F%)vS!x;K7gDmAZbjk2qcpAL6O}s9JVYoH_KR&FFGm88P7o`9$fJr2U zql?QroMiK}xywht`~+N4*8SH-L2aqDRWh5Gb@ Date: Wed, 31 Aug 2022 13:57:56 +0100 Subject: [PATCH 3/9] naming --- test/DCEmodels/test_DCEmodels_etofts_OGJ_OsloU_NOR.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/test/DCEmodels/test_DCEmodels_etofts_OGJ_OsloU_NOR.py b/test/DCEmodels/test_DCEmodels_etofts_OGJ_OsloU_NOR.py index 76f7567c..42598a90 100644 --- a/test/DCEmodels/test_DCEmodels_etofts_OGJ_OsloU_NOR.py +++ b/test/DCEmodels/test_DCEmodels_etofts_OGJ_OsloU_NOR.py @@ -3,7 +3,8 @@ from time import perf_counter from ..helpers import osipi_parametrize, log_init, log_results from . import DCEmodels_data -from osipi_code_collection.original.OGJ_OsloU_Norway.MRImageAnalysis.DCE.Analyze import fitToModel +from osipi_code_collection.original.OGJ_OsloU_NOR.MRImageAnalysis.DCE.Analyze \ + import fitToModel # All tests will use the same arguments and same data... arg_names = 'label, t_array, C_array, ca_array, ta_array, ve_ref, vp_ref, Ktrans_ref, arterial_delay_ref, a_tol_ve, ' \ From 4a2611be4fece1c14f6192a7ff4bae5be36f9018 Mon Sep 17 00:00:00 2001 From: mjt320 Date: Wed, 31 Aug 2022 14:16:03 +0100 Subject: [PATCH 4/9] naming --- src/wrappers/tofts.py | 2 +- .../test_DCEmodels_etofts_OG_MO_AUMC_ICR_RMH_ND_UK.py | 4 +++- test/SI_to_Conc/test_SI2Conc_OG_MO_AUMC_ICR_RMH_ND_UK.py | 4 ++-- test/T1_mapping/test_t1_OG_MO_AUMC_ICR_RMH_ND_UK.py | 2 +- 4 files changed, 7 insertions(+), 5 deletions(-) diff --git a/src/wrappers/tofts.py b/src/wrappers/tofts.py index 937688a7..f83c2eaa 100644 --- a/src/wrappers/tofts.py +++ b/src/wrappers/tofts.py @@ -14,7 +14,7 @@ import osipi_code_collection.original.ST_USydAUS.ModelDictionary as sydney from osipi_code_collection.original.MB_QBI_UoManchesterUK.QbiPy.dce_models import dce_aif as manchester_aif from osipi_code_collection.original.MB_QBI_UoManchesterUK.QbiPy.dce_models import tofts_model as manchester_tofts -import osipi_code_collection.original.OG_MO_AUMC_ICR_RMH.ExtendedTofts.DCE as amsterdam +import osipi_code_collection.original.OG_MO_AUMC_ICR_RMH_ND_UK.ExtendedTofts.DCE as amsterdam def tofts_fit(author, ct = None, ca = None, t = None, fittype = "linear", mask = None, data = None): # Author can be: edinburgh1, edinburgh2, sydney, amsterdam, oslo, manchester diff --git a/test/DCEmodels/test_DCEmodels_etofts_OG_MO_AUMC_ICR_RMH_ND_UK.py b/test/DCEmodels/test_DCEmodels_etofts_OG_MO_AUMC_ICR_RMH_ND_UK.py index 6ae5a13b..27cd31b6 100644 --- a/test/DCEmodels/test_DCEmodels_etofts_OG_MO_AUMC_ICR_RMH_ND_UK.py +++ b/test/DCEmodels/test_DCEmodels_etofts_OG_MO_AUMC_ICR_RMH_ND_UK.py @@ -3,7 +3,9 @@ from time import perf_counter from ..helpers import osipi_parametrize, log_init, log_results from . import DCEmodels_data -from osipi_code_collection.original.OG_MO_AUMC_ICR_RMH.ExtendedTofts.DCE import fit_tofts_model, fit_aif +from osipi_code_collection.original.OG_MO_AUMC_ICR_RMH_NL_UK.ExtendedTofts.DCE \ + import \ + fit_tofts_model, fit_aif # All tests will use the same arguments and same data... arg_names = 'label, t_array, C_array, ca_array, ta_array, ve_ref, vp_ref, Ktrans_ref, arterial_delay_ref, a_tol_ve, ' \ diff --git a/test/SI_to_Conc/test_SI2Conc_OG_MO_AUMC_ICR_RMH_ND_UK.py b/test/SI_to_Conc/test_SI2Conc_OG_MO_AUMC_ICR_RMH_ND_UK.py index 2bfe5100..51001093 100644 --- a/test/SI_to_Conc/test_SI2Conc_OG_MO_AUMC_ICR_RMH_ND_UK.py +++ b/test/SI_to_Conc/test_SI2Conc_OG_MO_AUMC_ICR_RMH_ND_UK.py @@ -4,8 +4,8 @@ from time import perf_counter from ..helpers import osipi_parametrize, log_init, log_results from . import SI2Conc_data -from osipi_code_collection.original.OG_MO_AUMC_ICR_RMH.ExtendedTofts.DCE import dce_to_r1eff -from osipi_code_collection.original.OG_MO_AUMC_ICR_RMH.ExtendedTofts.DCE import r1eff_to_conc +from osipi_code_collection.original.OG_MO_AUMC_ICR_RMH_ND_UK.ExtendedTofts.DCE import dce_to_r1eff +from osipi_code_collection.original.OG_MO_AUMC_ICR_RMH_ND_UK.ExtendedTofts.DCE import r1eff_to_conc diff --git a/test/T1_mapping/test_t1_OG_MO_AUMC_ICR_RMH_ND_UK.py b/test/T1_mapping/test_t1_OG_MO_AUMC_ICR_RMH_ND_UK.py index d6c91cb2..66ee318b 100644 --- a/test/T1_mapping/test_t1_OG_MO_AUMC_ICR_RMH_ND_UK.py +++ b/test/T1_mapping/test_t1_OG_MO_AUMC_ICR_RMH_ND_UK.py @@ -4,7 +4,7 @@ from time import perf_counter from ..helpers import osipi_parametrize, log_init, log_results from . import t1_data -from osipi_code_collection.original.OG_MO_AUMC_ICR_RMH.ExtendedTofts.DCE import R1_two_fas, R1_VFA +from osipi_code_collection.original.OG_MO_AUMC_ICR_RMH_ND_UK.ExtendedTofts.DCE import R1_two_fas, R1_VFA # All tests will use the same arguments and same data... From c7909386f03ba7cf90c886aab55d82f9b19abc04 Mon Sep 17 00:00:00 2001 From: mjt320 Date: Wed, 31 Aug 2022 14:20:21 +0100 Subject: [PATCH 5/9] naming --- src/wrappers/tofts.py | 2 +- ...py => test_DCEmodels_etofts_OG_MO_AUMC_ICR_RMH_NL_UK.py} | 4 ++-- ...MH_ND_UK.py => test_SI2Conc_OG_MO_AUMC_ICR_RMH_NL_UK.py} | 6 +++--- ...ICR_RMH_ND_UK.py => test_t1_OG_MO_AUMC_ICR_RMH_NL_UK.py} | 6 +++--- 4 files changed, 9 insertions(+), 9 deletions(-) rename test/DCEmodels/{test_DCEmodels_etofts_OG_MO_AUMC_ICR_RMH_ND_UK.py => test_DCEmodels_etofts_OG_MO_AUMC_ICR_RMH_NL_UK.py} (98%) rename test/SI_to_Conc/{test_SI2Conc_OG_MO_AUMC_ICR_RMH_ND_UK.py => test_SI2Conc_OG_MO_AUMC_ICR_RMH_NL_UK.py} (92%) rename test/T1_mapping/{test_t1_OG_MO_AUMC_ICR_RMH_ND_UK.py => test_t1_OG_MO_AUMC_ICR_RMH_NL_UK.py} (93%) diff --git a/src/wrappers/tofts.py b/src/wrappers/tofts.py index f83c2eaa..df11f76c 100644 --- a/src/wrappers/tofts.py +++ b/src/wrappers/tofts.py @@ -14,7 +14,7 @@ import osipi_code_collection.original.ST_USydAUS.ModelDictionary as sydney from osipi_code_collection.original.MB_QBI_UoManchesterUK.QbiPy.dce_models import dce_aif as manchester_aif from osipi_code_collection.original.MB_QBI_UoManchesterUK.QbiPy.dce_models import tofts_model as manchester_tofts -import osipi_code_collection.original.OG_MO_AUMC_ICR_RMH_ND_UK.ExtendedTofts.DCE as amsterdam +import osipi_code_collection.original.OG_MO_AUMC_ICR_RMH_NL_UK.ExtendedTofts.DCE as amsterdam def tofts_fit(author, ct = None, ca = None, t = None, fittype = "linear", mask = None, data = None): # Author can be: edinburgh1, edinburgh2, sydney, amsterdam, oslo, manchester diff --git a/test/DCEmodels/test_DCEmodels_etofts_OG_MO_AUMC_ICR_RMH_ND_UK.py b/test/DCEmodels/test_DCEmodels_etofts_OG_MO_AUMC_ICR_RMH_NL_UK.py similarity index 98% rename from test/DCEmodels/test_DCEmodels_etofts_OG_MO_AUMC_ICR_RMH_ND_UK.py rename to test/DCEmodels/test_DCEmodels_etofts_OG_MO_AUMC_ICR_RMH_NL_UK.py index 27cd31b6..95dcedaa 100644 --- a/test/DCEmodels/test_DCEmodels_etofts_OG_MO_AUMC_ICR_RMH_ND_UK.py +++ b/test/DCEmodels/test_DCEmodels_etofts_OG_MO_AUMC_ICR_RMH_NL_UK.py @@ -27,7 +27,7 @@ def setup_module(module): # Use the test data to generate a parametrize decorator. This causes the following # test to be run for every test case listed in test_data... @osipi_parametrize(arg_names, test_data, xf_labels=[]) -def test_OG_MO_AUMC_ICR_RMH_ND_UK_extended_tofts_kety_model(label, t_array, +def test_OG_MO_AUMC_ICR_RMH_NL_UK_extended_tofts_kety_model(label, t_array, C_array, ca_array, ta_array, ve_ref, vp_ref, Ktrans_ref, arterial_delay_ref, a_tol_ve, r_tol_ve, a_tol_vp, r_tol_vp, a_tol_Ktrans, r_tol_Ktrans, a_tol_delay, r_tol_delay): @@ -76,7 +76,7 @@ def test_OG_MO_AUMC_ICR_RMH_ND_UK_extended_tofts_kety_model(label, t_array, # Use the test data to generate a parametrize decorator. This causes the following # test to be run for every test case listed in test_data... @osipi_parametrize(arg_names, test_data_delay, xf_labels=[]) -def testOG_MO_AUMC_ICR_RMH_ND_UK_extended_tofts_kety_model_delay(label, t_array, +def testOG_MO_AUMC_ICR_RMH_NL_UK_extended_tofts_kety_model_delay(label, t_array, C_array, ca_array, ta_array, ve_ref, vp_ref, Ktrans_ref, arterial_delay_ref, a_tol_ve, r_tol_ve, a_tol_vp, r_tol_vp, a_tol_Ktrans, r_tol_Ktrans, a_tol_delay, r_tol_delay): diff --git a/test/SI_to_Conc/test_SI2Conc_OG_MO_AUMC_ICR_RMH_ND_UK.py b/test/SI_to_Conc/test_SI2Conc_OG_MO_AUMC_ICR_RMH_NL_UK.py similarity index 92% rename from test/SI_to_Conc/test_SI2Conc_OG_MO_AUMC_ICR_RMH_ND_UK.py rename to test/SI_to_Conc/test_SI2Conc_OG_MO_AUMC_ICR_RMH_NL_UK.py index 51001093..1b5fde3b 100644 --- a/test/SI_to_Conc/test_SI2Conc_OG_MO_AUMC_ICR_RMH_ND_UK.py +++ b/test/SI_to_Conc/test_SI2Conc_OG_MO_AUMC_ICR_RMH_NL_UK.py @@ -4,8 +4,8 @@ from time import perf_counter from ..helpers import osipi_parametrize, log_init, log_results from . import SI2Conc_data -from osipi_code_collection.original.OG_MO_AUMC_ICR_RMH_ND_UK.ExtendedTofts.DCE import dce_to_r1eff -from osipi_code_collection.original.OG_MO_AUMC_ICR_RMH_ND_UK.ExtendedTofts.DCE import r1eff_to_conc +from osipi_code_collection.original.OG_MO_AUMC_ICR_RMH_NL_UK.ExtendedTofts.DCE import dce_to_r1eff +from osipi_code_collection.original.OG_MO_AUMC_ICR_RMH_NL_UK.ExtendedTofts.DCE import r1eff_to_conc @@ -26,7 +26,7 @@ def setup_module(module): # Use the test data to generate a parametrize decorator. This causes the following # test to be run for every test case listed in test_data... @osipi_parametrize(arg_names, test_data, xf_labels = []) -def test_OG_MO_AUMC_ICR_RMH_ND_UK_SI2Conc(label, fa, tr, T1base, +def test_OG_MO_AUMC_ICR_RMH_NL_UK_SI2Conc(label, fa, tr, T1base, BLpts, r1, s_array, conc_array, a_tol, r_tol): # Note: the first signal value is not used for baseline estimation, # and the first C value is not logged or assessed diff --git a/test/T1_mapping/test_t1_OG_MO_AUMC_ICR_RMH_ND_UK.py b/test/T1_mapping/test_t1_OG_MO_AUMC_ICR_RMH_NL_UK.py similarity index 93% rename from test/T1_mapping/test_t1_OG_MO_AUMC_ICR_RMH_ND_UK.py rename to test/T1_mapping/test_t1_OG_MO_AUMC_ICR_RMH_NL_UK.py index 66ee318b..94239a5a 100644 --- a/test/T1_mapping/test_t1_OG_MO_AUMC_ICR_RMH_ND_UK.py +++ b/test/T1_mapping/test_t1_OG_MO_AUMC_ICR_RMH_NL_UK.py @@ -4,7 +4,7 @@ from time import perf_counter from ..helpers import osipi_parametrize, log_init, log_results from . import t1_data -from osipi_code_collection.original.OG_MO_AUMC_ICR_RMH_ND_UK.ExtendedTofts.DCE import R1_two_fas, R1_VFA +from osipi_code_collection.original.OG_MO_AUMC_ICR_RMH_NL_UK.ExtendedTofts.DCE import R1_two_fas, R1_VFA # All tests will use the same arguments and same data... @@ -30,7 +30,7 @@ def setup_module(module): # test to be run for every test case listed in test_data... # In the following test, we specify 1 case that is expected to fail... @osipi_parametrize(arg_names, test_data, xf_labels = ['Pat5_voxel5_prostaat']) -def test_OG_MO_AUMC_ICR_RMH_ND_UK_t1_VFA_2fa(label, fa_array, tr_array, +def test_OG_MO_AUMC_ICR_RMH_NL_UK_t1_VFA_2fa(label, fa_array, tr_array, s_array, r1_ref, s0_ref, a_tol, r_tol): # NOTES: # Code requires signal array with min 2 dimensions (including FA) @@ -52,7 +52,7 @@ def test_OG_MO_AUMC_ICR_RMH_ND_UK_t1_VFA_2fa(label, fa_array, tr_array, @osipi_parametrize(arg_names, test_data, xf_labels=[]) -def test_OG_MO_AUMC_ICR_RMH_ND_UK_t1_VFA(label, fa_array, tr_array, s_array, +def test_OG_MO_AUMC_ICR_RMH_NL_UK_t1_VFA(label, fa_array, tr_array, s_array, r1_ref, s0_ref, a_tol, r_tol): # NOTES: # Code requires signal array with min 2 dimensions (including FA) From 3143969df3361b8d6fa7ce40267ae8c2108c9472 Mon Sep 17 00:00:00 2001 From: mjt320 Date: Wed, 31 Aug 2022 14:50:24 +0100 Subject: [PATCH 6/9] naming --- doc/code_contributions_record.csv | 16 ++++---- notebooks/DSC_pars.ipynb | 6 +-- notebooks/contributors.ipynb | 40 +++++++++---------- .../test_DCEmodels_tofts_LCB_BNI_USA.py | 6 +-- ...SCmodels_LcurveReg_SR_TBG_BNIPhoenixUSA.py | 10 ++--- test/SI_to_Conc/test_SI2Conc_LCB_BNI_USA.py | 6 +-- test/results-meta.json | 8 ++-- 7 files changed, 46 insertions(+), 46 deletions(-) diff --git a/doc/code_contributions_record.csv b/doc/code_contributions_record.csv index 0d55bfbf..1b875500 100644 --- a/doc/code_contributions_record.csv +++ b/doc/code_contributions_record.csv @@ -20,7 +20,7 @@ DCE,Miscellaneous,enhancement detection,check for enhancement,OG_MO_AUMC_ICR_RMH DCE,Parameter derivation,iAUC,,MB_QBI_UoManchesterUK,Michael Berks,"University of Manchester, UK",compute_IAUC,https://doi.org/10.21105/joss.03523,tbd, DCE,Pharmacokinetic models,Tofts,NLLS fitting (+forward model),DS_BW_VanderBiltUMC_USA,"David Smith, Brian Welch","VanderBilt University Medical Center, USA","tofts_integral, fit_tofts_model",,tdd, DCE,Pharmacokinetic models,extended Tofts,NLLS fitting (+forward model),DS_BW_VanderBiltUMC_USA,"David Smith, Brian Welch","VanderBilt University Medical Center, USA","ext_tofts_integral, fit_tofts_model",,tbd, -DCE,Pharmacokinetic models,Tofts,NLLS fitting (+ forward model),LCB_BNI,Laura Bell,"Barrow Neurological Institute, USA","tofts_model, fit_tofts",,ST/OGC,completed +DCE,Pharmacokinetic models,Tofts,NLLS fitting (+ forward model),LCB_BNI_USA,Laura Bell,"Barrow Neurological Institute, USA","tofts_model, fit_tofts",,ST/OGC,completed DCE,Pharmacokinetic models,2-cmp exchange,forward model,LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",TwoCXM,,MJT,completed DCE,Pharmacokinetic models,2-cmp uptake,forward model,LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",TwoCUM,,MJT,completed DCE,Pharmacokinetic models,AATH,forward model,LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",AATH,,tbd, @@ -60,7 +60,7 @@ DCE,Pharmacokinetic models,Tofts,forward model,ST_USydAUS_DCE,Sirisha Tadimalla, DCE,Pharmacokinetic models,high flow 2-cmp Gadoxetate,forward model,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",,,tbd, DCE,Pharmacokinetic models,Patlak,forward model,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",PatlakModel,,MJT,completed DCE,Signal to Concentration,SPGR,"two-steps: S->R1, R1->C",DS_BW_VanderBiltUMC_USA,"David Smith, Brian Welch","VanderBilt University Medical Center, USA","r1eff_to_conc, dce_to_r1eff",,tbd, -DCE,Signal to Concentration,SPGR or GE-EPI,,LCB_BNI,Laura Bell,"Barrow Neurological Institute, USA","signal_to_conc, estimate_delta_R1",,LK,completed +DCE,Signal to Concentration,SPGR or GE-EPI,,LCB_BNI_USA,Laura Bell,"Barrow Neurological Institute, USA","signal_to_conc, estimate_delta_R1",,LK,completed DCE,Signal to concentration,SPGR,"reverse C->S also available",LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",SI2Conc,,LK,completed DCE,Signal to concentration,SPGR,"reverse C->S also available",MB_QBI_UoManchesterUK,Michael Berks,"University of Manchester, UK",signal_to_concentration,https://doi.org/10.21105/joss.03523,LK,completed DCE,Signal to concentration,SPGR,"two steps: S-> enhancement, enhancement -> C; reverse C->S also available",MJT_UoEdinburghUK,Michael Thrippleton,"University of Edinburgh, UK","sign_to_enh, enh_to_conc",,LK,completed @@ -77,12 +77,12 @@ DCE,T1,VFA,two flip angles (linear),OG_MO_AUMC_ICR_RMH,"Oliver Gurney-Champion, DCE,T1,VFA,nonlinear,OG_MO_AUMC_ICR_RMH,"Oliver Gurney-Champion, Matthew Orton","Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK",R1_VFA,,MJT,competed DCE,T1,VFA,linear,ST_SydneyAus_T1,Sirisha Tadimalla,"University of Sydney, Australia",VFAT1mapping,,MJT,completed DCE,T1,VFA,nonlinear,ST_SydneyAus_T1,Sirisha Tadimalla,"University of Sydney, Australia",VFAT1mapping,,MJT,completed -DCE/DSC,AIF deconvolution,,,SR_TBG_BNIPhoenixUSA,"Sudarshan Ragunathan, Laura Bell","Barrow Neurological Institute, USA",AIFdeconvolution,,JA,completed +DCE/DSC,AIF deconvolution,,,SR_TBG_BNI_USAPhoenixUSA,"Sudarshan Ragunathan, Laura Bell","Barrow Neurological Institute, USA",AIFdeconvolution,,JA,completed DCE/DSC,Miscellaneous,calculate SNR,,DS_BW_VanderBiltUMC_USA,"David Smith, Brian Welch","VanderBilt University Medical Center, USA",signal_to_noise_ratio,,tbd, DCE/DSC,Miscellaneous,calculate enhancement ratio,,DS_BW_VanderBiltUMC_USA,"David Smith, Brian Welch","VanderBilt University Medical Center, USA",signal_enhancement_ratio,,tbd, DSC,Input Functions,automatic AIF selection,"fully automatic, semi-automatic",JBJA_GUSahlgrenskaSWE,"Jesper Browall, Jonathan Arvidsson","Sahlgrenska University Hospital and Gothenburg University, Gothenburg, Sweden",AIF_selection_automatic.py,DOI: 10.1002/mrm.20759,tbd, -DSC,Leakage correction,BSW,,SR_TBG_BNIPhoenixUSA,"Sudarshan Ragunathan, Laura Bell","Barrow Neurological Institute, USA",BSWleakagecorr,,SR,in-progress -DSC,Parameter derivation,"CBV,CBF,MTT",,SR_TBG_BNIPhoenixUSA,"Sudarshan Ragunathan, Laura Bell","Barrow Neurological Institute, USA",DSCparameters,,tbd, -DSC,Signal to deltaR2*,single echo,,LCB_BNI,Laura Bell,"Barrow Neurological Institute, USA",,estimate_delta_R2s,tbd, -DSC,Signal to deltaR2*,dual echo,,LCB_BNI,Laura Bell,"Barrow Neurological Institute, USA",,"estimate_delta_R2s, estimate_delta_R2s_dual_echo",tbd, -DSC,Signal to R2*,dual echo,,LCB_BNI,Laura Bell,"Barrow Neurological Institute, USA",,estimate_R2s,tbd, \ No newline at end of file +DSC,Leakage correction,BSW,,SR_TBG_BNI_USAPhoenixUSA,"Sudarshan Ragunathan, Laura Bell","Barrow Neurological Institute, USA",BSWleakagecorr,,SR,in-progress +DSC,Parameter derivation,"CBV,CBF,MTT",,SR_TBG_BNI_USAPhoenixUSA,"Sudarshan Ragunathan, Laura Bell","Barrow Neurological Institute, USA",DSCparameters,,tbd, +DSC,Signal to deltaR2*,single echo,,LCB_BNI_USA,Laura Bell,"Barrow Neurological Institute, USA",,estimate_delta_R2s,tbd, +DSC,Signal to deltaR2*,dual echo,,LCB_BNI_USA,Laura Bell,"Barrow Neurological Institute, USA",,"estimate_delta_R2s, estimate_delta_R2s_dual_echo",tbd, +DSC,Signal to R2*,dual echo,,LCB_BNI_USA,Laura Bell,"Barrow Neurological Institute, USA",,estimate_R2s,tbd, \ No newline at end of file diff --git a/notebooks/DSC_pars.ipynb b/notebooks/DSC_pars.ipynb index eed2c83d..4f187f65 100644 --- a/notebooks/DSC_pars.ipynb +++ b/notebooks/DSC_pars.ipynb @@ -199,7 +199,7 @@ "source": [ "If the tolerance lines are not shown, it means that they are outside the limits of the y-axis.\n", "\n", - "The contribution by SR_TBG_BNIPhoenix uses the L-curve criterion (for more information see doi:10.1088/0031-9155/52/2/009). Additional tag was added to the contribution to indicate the method (LCC SFTR) " + "The contribution by SR_TBG_BNI_USAPhoenix uses the L-curve criterion (for more information see doi:10.1088/0031-9155/52/2/009). Additional tag was added to the contribution to indicate the method (LCC SFTR) " ] }, { @@ -271,7 +271,7 @@ "text": [ " bias stdev LoA lower LoA upper\n", "author \n", - "SR_LB_TBG_BNIPhoenix_USA_LCC SFTR 0.312242 0.236365 -0.151033 0.775517\n" + "SR_LB_TBG_BNI_USAPhoenix_USA_LCC SFTR 0.312242 0.236365 -0.151033 0.775517\n" ] } ], @@ -300,7 +300,7 @@ "text": [ " bias stdev LoA lower LoA upper\n", "author \n", - "SR_LB_TBG_BNIPhoenix_USA_LCC SFTR -2.93965 4.107339 -10.990034 5.110734\n" + "SR_LB_TBG_BNI_USAPhoenix_USA_LCC SFTR -2.93965 4.107339 -10.990034 5.110734\n" ] } ], diff --git a/notebooks/contributors.ipynb b/notebooks/contributors.ipynb index acf9e357..d8cb90ff 100644 --- a/notebooks/contributors.ipynb +++ b/notebooks/contributors.ipynb @@ -700,7 +700,7 @@ " Pharmacokinetic models\n", " Tofts\n", " forward model, NLLS fitting methods\n", - " LCB_BNI\n", + " LCB_BNI_USA\n", " Laura Bell\n", " Barrow Neurological Institute, USA\n", " ST/OGC\n", @@ -817,7 +817,7 @@ " Signal to concentration\n", " SPGR or GE-EPI\n", " NaN\n", - " LCB_BNI\n", + " LCB_BNI_USA\n", " Laura Bell\n", " Barrow Neurological Institute, USA\n", " LK\n", @@ -869,7 +869,7 @@ " Signal to R1\n", " SPGR or GE-EPI\n", " NaN\n", - " LCB_BNI\n", + " LCB_BNI_USA\n", " Laura Bell\n", " Barrow Neurological Institute, USA\n", " tbd\n", @@ -947,7 +947,7 @@ " AIF deconvolution\n", " NaN\n", " NaN\n", - " SR_TBG_BNIPhoenixUSA\n", + " SR_TBG_BNI_USAPhoenixUSA\n", " Sudarshan Ragunathan\n", " Barrow Neurological Institute, USA\n", " tbd\n", @@ -973,7 +973,7 @@ " Leakage correction\n", " BSW\n", " NaN\n", - " SR_TBG_BNIPhoenixUSA\n", + " SR_TBG_BNI_USAPhoenixUSA\n", " Sudarshan Ragunathan\n", " Barrow Neurological Institute, USA\n", " tbd\n", @@ -986,7 +986,7 @@ " Leakage correction\n", " BSW\n", " NaN\n", - " LCB_BNI\n", + " LCB_BNI_USA\n", " Laura Bell\n", " Barrow Neurological Institute, USA\n", " tbd\n", @@ -999,7 +999,7 @@ " Parameter derivation\n", " CBV,CBF,MTT\n", " NaN\n", - " LCB_BNI\n", + " LCB_BNI_USA\n", " Laura Bell\n", " Barrow Neurological Institute, USA\n", " tbd\n", @@ -1012,7 +1012,7 @@ " Parameter derivation\n", " CBV,CBF,MTT\n", " NaN\n", - " SR_TBG_BNIPhoenixUSA\n", + " SR_TBG_BNI_USAPhoenixUSA\n", " Sudarshan Ragunathan\n", " Barrow Neurological Institute, USA\n", " tbd\n", @@ -1025,7 +1025,7 @@ " Signal to deltaR2*\n", " single echo, dual echo\n", " NaN\n", - " LCB_BNI\n", + " LCB_BNI_USA\n", " Laura Bell\n", " Barrow Neurological Institute, USA\n", " tbd\n", @@ -1038,7 +1038,7 @@ " Signal to R2*\n", " dual echo\n", " NaN\n", - " LCB_BNI\n", + " LCB_BNI_USA\n", " Laura Bell\n", " Barrow Neurological Institute, USA\n", " tbd\n", @@ -1253,7 +1253,7 @@ "45 forward model LEK_UoEdinburgh \n", "46 forward model, NLLS and LLSQ fitting methods OGJ_OsloU_Norway \n", "47 forward model, NLLS fitting (concentration), N... MJT_UoEdinburghUK \n", - "48 forward model, NLLS fitting methods LCB_BNI \n", + "48 forward model, NLLS fitting methods LCB_BNI_USA \n", "49 check for enhancement OG_MO_AUMC_ICR_RMH \n", "50 NaN OG_MO_AUMC_ICR_RMH \n", "51 NaN ST_USydAUS_DCE \n", @@ -1262,24 +1262,24 @@ "54 NaN ST_USydAUS_DCE \n", "55 NaN MJT_UoEdinburghUK \n", "56 NaN MB_QBI_UoManchesterUK \n", - "57 NaN LCB_BNI \n", + "57 NaN LCB_BNI_USA \n", "58 NaN MJT_UoEdinburghUK \n", "59 NaN ST_USydAUS_DCE \n", "60 NaN OG_MO_AUMC_ICR_RMH \n", - "61 NaN LCB_BNI \n", + "61 NaN LCB_BNI_USA \n", "62 Fit any combination of (IR-)SPGR scans to esti... MJT_UoEdinburghUK \n", "63 linear, nonlinear ST_SydneyAus_T1 \n", "64 linear, nonlinear, two flip angles MJT_UoEdinburghUK \n", "65 two flip angles OG_MO_AUMC_ICR_RMH \n", "66 despot, novifast McGill_VFA \n", - "67 NaN SR_TBG_BNIPhoenixUSA \n", + "67 NaN SR_TBG_BNI_USAPhoenixUSA \n", "68 fully automatic, semi-automatic JBJA_GUSahlgrenskaSWE \n", - "69 NaN SR_TBG_BNIPhoenixUSA \n", - "70 NaN LCB_BNI \n", - "71 NaN LCB_BNI \n", - "72 NaN SR_TBG_BNIPhoenixUSA \n", - "73 NaN LCB_BNI \n", - "74 NaN LCB_BNI \n", + "69 NaN SR_TBG_BNI_USAPhoenixUSA \n", + "70 NaN LCB_BNI_USA \n", + "71 NaN LCB_BNI_USA \n", + "72 NaN SR_TBG_BNI_USAPhoenixUSA \n", + "73 NaN LCB_BNI_USA \n", + "74 NaN LCB_BNI_USA \n", "\n", " Authors \\\n", "0 Lucy Kershaw \n", diff --git a/test/DCEmodels/test_DCEmodels_tofts_LCB_BNI_USA.py b/test/DCEmodels/test_DCEmodels_tofts_LCB_BNI_USA.py index 7bf98ec9..0b190ce1 100644 --- a/test/DCEmodels/test_DCEmodels_tofts_LCB_BNI_USA.py +++ b/test/DCEmodels/test_DCEmodels_tofts_LCB_BNI_USA.py @@ -3,7 +3,7 @@ from time import perf_counter from ..helpers import osipi_parametrize, log_init, log_results from . import DCEmodels_data -from osipi_code_collection.original.LCB_BNI.dce import fit_tofts +from osipi_code_collection.original.LCB_BNI_USA.dce import fit_tofts arg_names = 'label, t_array, C_array, ca_array, ta_array, ve_ref, Ktrans_ref, arterial_delay_ref, a_tol_ve, r_tol_ve, ' \ 'a_tol_Ktrans, r_tol_Ktrans, a_tol_delay, r_tol_delay ' @@ -17,7 +17,7 @@ def setup_module(module): global filename_prefix # we want to change the global variable os.makedirs('./test/results/DCEmodels', exist_ok=True) filename_prefix = 'DCEmodels/TestResults_models' - log_init(filename_prefix, '_LCB_BNI_tofts', ['label', 'time (us)', 'Ktrans_ref', 've_ref', 'Ktrans_meas', 've_meas']) + log_init(filename_prefix, '_LCB_BNI_USA_tofts', ['label', 'time (us)', 'Ktrans_ref', 've_ref', 'Ktrans_meas', 've_meas']) # Use the test data to generate a parametrize decorator. This causes the following test to be run for every test case @@ -37,7 +37,7 @@ def test_LCB_BNI_USA_tofts_model(label, t_array, C_array, ca_array, ta_array, exc_time = 1e6 * (perf_counter() - tic) # measure execution time # log results - log_results(filename_prefix, '_LCB_BNI_tofts', [ + log_results(filename_prefix, '_LCB_BNI_USA_tofts', [ [label, f"{exc_time:.0f}", Ktrans_ref, ve_ref, Ktrans_meas, ve_meas]]) # run test diff --git a/test/DSCmodels/test_DSCmodels_LcurveReg_SR_TBG_BNIPhoenixUSA.py b/test/DSCmodels/test_DSCmodels_LcurveReg_SR_TBG_BNIPhoenixUSA.py index 5a1a4e57..db0a9948 100644 --- a/test/DSCmodels/test_DSCmodels_LcurveReg_SR_TBG_BNIPhoenixUSA.py +++ b/test/DSCmodels/test_DSCmodels_LcurveReg_SR_TBG_BNIPhoenixUSA.py @@ -3,8 +3,8 @@ from time import perf_counter from ..helpers import osipi_parametrize, log_init, log_results from . import DSCmodels_data -from src.original.SR_TBG_BNIPhoenixUSA.AIFDeconvolution.AIF_deconvolution import AIFdeconvolution -from src.original.SR_TBG_BNIPhoenixUSA.DSCparameters.DSC_parameters import DSCparameters +from src.original.SR_TBG_BNI_USAPhoenixUSA.AIFDeconvolution.AIF_deconvolution import AIFdeconvolution +from src.original.SR_TBG_BNI_USAPhoenixUSA.DSCparameters.DSC_parameters import DSCparameters # All tests will use the same arguments and same data... arg_names = 'label, C_tis, C_aif, tr, cbv_ref, cbf_ref,' \ @@ -20,12 +20,12 @@ def setup_module(module): global filename_prefix # we want to change the global variable os.makedirs('./test/results/DSCmodels', exist_ok=True) filename_prefix = 'DSCmodels/TestResults_ParamEstimation' - log_init(filename_prefix, '_SR_TBG_BNIPhoenix_USA', ['label', 'time (us)', 'cbv_ref', 'cbf_ref', 'cbv_meas', 'cbf_meas']) + log_init(filename_prefix, '_SR_TBG_BNI_USAPhoenix_USA', ['label', 'time (us)', 'cbv_ref', 'cbf_ref', 'cbv_meas', 'cbf_meas']) # Use the test data to generate a parametrize decorator. This causes the following test to be run for every test case # listed in test_data... @osipi_parametrize(arg_names, test_data, xf_labels=[]) -def test_SR_TBG_BNIPhoenixUSA_LcurveReg(label, C_tis, C_aif, tr, cbv_ref, cbf_ref, +def test_SR_TBG_BNI_USAPhoenixUSA_LcurveReg(label, C_tis, C_aif, tr, cbv_ref, cbf_ref, r_tol_cbv, r_tol_cbf, a_tol_cbv, a_tol_cbf): # run code @@ -35,7 +35,7 @@ def test_SR_TBG_BNIPhoenixUSA_LcurveReg(label, C_tis, C_aif, tr, cbv_ref, cbf_re exc_time = 1e6 * (perf_counter() - tic) # measure execution time # log results - log_results(filename_prefix, '_SR_TBG_BNIPhoenix_USA', [ + log_results(filename_prefix, '_SR_TBG_BNI_USAPhoenix_USA', [ [label, f"{exc_time:.0f}", cbv_ref, cbf_ref, cbv_meas, cbf_meas]]) # run test diff --git a/test/SI_to_Conc/test_SI2Conc_LCB_BNI_USA.py b/test/SI_to_Conc/test_SI2Conc_LCB_BNI_USA.py index 708ecb21..06ffc8c2 100644 --- a/test/SI_to_Conc/test_SI2Conc_LCB_BNI_USA.py +++ b/test/SI_to_Conc/test_SI2Conc_LCB_BNI_USA.py @@ -4,7 +4,7 @@ from time import perf_counter from ..helpers import osipi_parametrize, log_init, log_results from . import SI2Conc_data -from osipi_code_collection.original.LCB_BNI.dce import signal_to_conc +from osipi_code_collection.original.LCB_BNI_USA.dce import signal_to_conc # All tests will use the same arguments and same data... @@ -18,7 +18,7 @@ def setup_module(module): global filename_prefix # we want to change the global variable os.makedirs('./test/results/SI_to_Conc', exist_ok=True) filename_prefix = 'SI_to_Conc/TestResults_SI2Conc' - log_init(filename_prefix, '_LCB_BNI', ['label', 'time (us)', 'conc_ref', 'conc_meas']) + log_init(filename_prefix, '_LCB_BNI_USA', ['label', 'time (us)', 'conc_ref', 'conc_meas']) # Use the test data to generate a parametrize decorator. This causes the following @@ -39,7 +39,7 @@ def test_LCB_BNI_USA_SI2Conc(label, fa, tr, T1base, BLpts, r1, row_data = [] for ref, meas in zip(conc_array[1:], conc_curve[1:]): row_data.append([label, f"{exc_time:.0f}", ref, meas]) - log_results(filename_prefix, '_LCB_BNI', row_data) + log_results(filename_prefix, '_LCB_BNI_USA', row_data) # testing np.testing.assert_allclose(conc_curve[1:], conc_array[1:], rtol=r_tol, diff --git a/test/results-meta.json b/test/results-meta.json index 31ba5b06..c71e8c12 100644 --- a/test/results-meta.json +++ b/test/results-meta.json @@ -65,7 +65,7 @@ }, { "path": "../test/results/SI_to_Conc", - "filename": "TestResults_SI2Conc_LCB_BNI.csv", + "filename": "TestResults_SI2Conc_LCB_BNI_USA.csv", "category": "SI_to_Conc", "method": "", "author": "LCB_BNI_USA" @@ -156,7 +156,7 @@ }, { "path": "../test/results/DCEmodels", - "filename": "TestResults_models_LCB_BNI_tofts.csv", + "filename": "TestResults_models_LCB_BNI_USA_tofts.csv", "category": "DCEmodels", "method": "tofts", "author": "LCB_BNI_USA" @@ -317,9 +317,9 @@ }, { "path": "../test/results/DSCmodels", - "filename": "TestResults_ParamEstimation_SR_TBG_BNIPhoenix_USA.csv", + "filename": "TestResults_ParamEstimation_SR_TBG_BNI_USAPhoenix_USA.csv", "category": "DSCmodels", "method": "", - "author": "SR_LB_TBG_BNIPhoenix_USA_LCC SFTR" + "author": "SR_LB_TBG_BNI_USAPhoenix_USA_LCC SFTR" } ] \ No newline at end of file From 4df502b2dd1c95ffda8151f21c9e35239b33f124 Mon Sep 17 00:00:00 2001 From: mjt320 Date: Wed, 31 Aug 2022 14:53:25 +0100 Subject: [PATCH 7/9] naming --- doc/code_contributions_record.csv | 14 +++++++------- notebooks/ExtendedToftsModel.ipynb | 2 +- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/doc/code_contributions_record.csv b/doc/code_contributions_record.csv index 1b875500..0865948b 100644 --- a/doc/code_contributions_record.csv +++ b/doc/code_contributions_record.csv @@ -10,8 +10,8 @@ DCE,Input Functions,Heye AIF,Heye et al (https://doi.org/10.1016/j.neuroimage.20 DCE,Input Functions,AIF parameterization,,OG_MO_AUMC_ICR_RMH,"Oliver Gurney-Champion, Matthew Orton","Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK","Cosine4AIF, Cosine8AIF",https://doi.org/10.1088/0031-9155/53/5/005; https://doi.org/10.1007/s00330-015-4012-9,tbd, DCE,Input Functions,Head-and-neck population AIF,Wong et al (DOI: https://doi.org/10.2967/jnumed.116.174433),OG_MO_AUMC_ICR_RMH,"Oliver Gurney-Champion, Matthew Orton","Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK",aifPopHN,,tbd, DCE,Input Functions,Parker AIF,,OG_MO_AUMC_ICR_RMH,"Oliver Gurney-Champion, Matthew Orton","Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK",aifPopPMB,,tbd, -DCE,Input Functions,load AIF,from txt,OGJ_OsloU_Norway,Ole Gunnar Johansen,"University of Oslo, Norway",loadStandard,,tbd, -DCE,Input Functions,AIF parameterization,fit gamma-variate function,OGJ_OsloU_Norway,Ole Gunnar Johansen,"University of Oslo, Norway",gammaVariateFit,,tbd, +DCE,Input Functions,load AIF,from txt,OGJ_OsloU_NOR,Ole Gunnar Johansen,"University of Oslo, Norway",loadStandard,,tbd, +DCE,Input Functions,AIF parameterization,fit gamma-variate function,OGJ_OsloU_NOR,Ole Gunnar Johansen,"University of Oslo, Norway",gammaVariateFit,,tbd, DCE,Input Functions,Georgiou AIF,Georgiou et al (DOI: 10.1002/mrm.27524),PvH_NKI,Petra van Houdt,"the Netherlands Cancer Institute, the Netherlands",GeorgiouAIF,,JK/PvH,completed DCE,Input Functions,Parker AIF,,PvH_NKI,Petra van Houdt,"the Netherlands Cancer Institute, the Netherlands",ParkerAIF,,JK/PvH,completed DCE,Input Functions,Parker AIF,,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia","AIF, variableAIF",,JK/PvH,completed @@ -46,11 +46,11 @@ DCE,Pharmacokinetic models,steady-state vp,NLLS fitting to signal incl. water ex DCE,Pharmacokinetic models,Tofts,NLLS fitting to concentration values (incl forward model),MJT_UoEdinburghUK,Michael Thrippleton,"University of Edinburgh, UK","Tofts, EnhToPKP, ConcToPKP",,ST/OGC,completed DCE,Pharmacokinetic models,Tofts,NLLS fitting to signal incl. water exchange (incl forward model),MJT_UoEdinburghUK,Michael Thrippleton,"University of Edinburgh, UK","Tofts,EnhToPKP, ConcToPKP",,ST/OGC,completed DCE,Pharmacokinetic models,extended Tofts,NLLS fitting (+forward model),OG_MO_AUMC_ICR_RMH,"Oliver Gurney-Champion, Matthew Orton","Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK",fit_tofts_model,,ST/OGC,completed -DCE,Pharmacokinetic models,2-cmp exchange,LLSQ fitting (+ forward model),OGJ_OsloU_Norway,Ole Gunnar Johansen,"University of Oslo, Norway","twoCXM, fitToModelLLSQ",,MJT,completed -DCE,Pharmacokinetic models,extended Tofts,NLLS fitting (+ forward model),OGJ_OsloU_Norway,Ole Gunnar Johansen,"University of Oslo, Norway","ETM, fitToModelNLLS, fitToModelNLLS_parallel",,ST/OGC,completed -DCE,Pharmacokinetic models,extended Tofts,LLSQ fitting (+ forward model),OGJ_OsloU_Norway,Ole Gunnar Johansen,"University of Oslo, Norway","ETM, fitToModelLLSQ",,ST/OGC,completed -DCE,Pharmacokinetic models,Tofts,NLLS fitting (+ forward model),OGJ_OsloU_Norway,Ole Gunnar Johansen,"University of Oslo, Norway","TM, fitToModelNLLS, fitToModelNLLS_parallel",,ST/OGC,completed -DCE,Pharmacokinetic models,Tofts,LLSQ fitting (+ forward model),OGJ_OsloU_Norway,Ole Gunnar Johansen,"University of Oslo, Norway","TM, fitToModelLLSQ",,ST/OGC,completed +DCE,Pharmacokinetic models,2-cmp exchange,LLSQ fitting (+ forward model),OGJ_OsloU_NOR,Ole Gunnar Johansen,"University of Oslo, Norway","twoCXM, fitToModelLLSQ",,MJT,completed +DCE,Pharmacokinetic models,extended Tofts,NLLS fitting (+ forward model),OGJ_OsloU_NOR,Ole Gunnar Johansen,"University of Oslo, Norway","ETM, fitToModelNLLS, fitToModelNLLS_parallel",,ST/OGC,completed +DCE,Pharmacokinetic models,extended Tofts,LLSQ fitting (+ forward model),OGJ_OsloU_NOR,Ole Gunnar Johansen,"University of Oslo, Norway","ETM, fitToModelLLSQ",,ST/OGC,completed +DCE,Pharmacokinetic models,Tofts,NLLS fitting (+ forward model),OGJ_OsloU_NOR,Ole Gunnar Johansen,"University of Oslo, Norway","TM, fitToModelNLLS, fitToModelNLLS_parallel",,ST/OGC,completed +DCE,Pharmacokinetic models,Tofts,LLSQ fitting (+ forward model),OGJ_OsloU_NOR,Ole Gunnar Johansen,"University of Oslo, NOR","TM, fitToModelLLSQ",,ST/OGC,completed DCE,Pharmacokinetic models,1-cmp,forward model,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",OneCompartment,,tbd, DCE,Pharmacokinetic models,dual-inlet 1-cmp,forward model,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",DualInletOneCompartment,,tbd, DCE,Pharmacokinetic models,dual-inlet ext Tofts,forward model,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",DualInletExtendedTofts,,tbd, diff --git a/notebooks/ExtendedToftsModel.ipynb b/notebooks/ExtendedToftsModel.ipynb index 8c8f5d6d..07c0067e 100644 --- a/notebooks/ExtendedToftsModel.ipynb +++ b/notebooks/ExtendedToftsModel.ipynb @@ -289,7 +289,7 @@ "Some models allow the fit of a delay. For the tests with non-delayed data, the delay was fixed to 0. \n", "The data are shown with a categorial swarm plot, so for each text voxel separately to better appreciate the differences between contributions. Note that, the x-axis is not a continuous axis, but has a label per test voxel. To get an idea of the reference values per test case, the table below refers as a legend for the figure. \n", "\n", - "Note that, one author (OGJ_OsloU_Norway) provided two options to fit the model (LLSQ and NLLS). These were considered separate contributions." + "Note that, one author (OGJ_OsloU_NOR) provided two options to fit the model (LLSQ and NLLS). These were considered separate contributions." ] }, { From a99516d780bd2aedb5a54a0ad7a7755758aa39e9 Mon Sep 17 00:00:00 2001 From: mjt320 Date: Wed, 31 Aug 2022 15:15:30 +0100 Subject: [PATCH 8/9] naming --- doc/code_contributions_record.csv | 6 +++--- notebooks/contributors.ipynb | 12 ++++++------ src/wrappers/tofts.py | 2 +- src/wrappers/vfa.py | 2 +- test/DCEmodels/test_DCEmodels_tofts_OGJ_OsloU_NOR.py | 2 +- .../test_DSCmodels_LcurveReg_SR_TBG_BNIPhoenixUSA.py | 6 +++--- test/T1_mapping/test_t1_ZA_McGill_CAN.py | 2 +- test/results-meta.json | 4 ++-- 8 files changed, 18 insertions(+), 18 deletions(-) diff --git a/doc/code_contributions_record.csv b/doc/code_contributions_record.csv index 0865948b..7e85457a 100644 --- a/doc/code_contributions_record.csv +++ b/doc/code_contributions_record.csv @@ -77,12 +77,12 @@ DCE,T1,VFA,two flip angles (linear),OG_MO_AUMC_ICR_RMH,"Oliver Gurney-Champion, DCE,T1,VFA,nonlinear,OG_MO_AUMC_ICR_RMH,"Oliver Gurney-Champion, Matthew Orton","Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK",R1_VFA,,MJT,competed DCE,T1,VFA,linear,ST_SydneyAus_T1,Sirisha Tadimalla,"University of Sydney, Australia",VFAT1mapping,,MJT,completed DCE,T1,VFA,nonlinear,ST_SydneyAus_T1,Sirisha Tadimalla,"University of Sydney, Australia",VFAT1mapping,,MJT,completed -DCE/DSC,AIF deconvolution,,,SR_TBG_BNI_USAPhoenixUSA,"Sudarshan Ragunathan, Laura Bell","Barrow Neurological Institute, USA",AIFdeconvolution,,JA,completed +DCE/DSC,AIF deconvolution,,,SR_TBG_BNI_PhoenixUSA,"Sudarshan Ragunathan, Laura Bell","Barrow Neurological Institute, USA",AIFdeconvolution,,JA,completed DCE/DSC,Miscellaneous,calculate SNR,,DS_BW_VanderBiltUMC_USA,"David Smith, Brian Welch","VanderBilt University Medical Center, USA",signal_to_noise_ratio,,tbd, DCE/DSC,Miscellaneous,calculate enhancement ratio,,DS_BW_VanderBiltUMC_USA,"David Smith, Brian Welch","VanderBilt University Medical Center, USA",signal_enhancement_ratio,,tbd, DSC,Input Functions,automatic AIF selection,"fully automatic, semi-automatic",JBJA_GUSahlgrenskaSWE,"Jesper Browall, Jonathan Arvidsson","Sahlgrenska University Hospital and Gothenburg University, Gothenburg, Sweden",AIF_selection_automatic.py,DOI: 10.1002/mrm.20759,tbd, -DSC,Leakage correction,BSW,,SR_TBG_BNI_USAPhoenixUSA,"Sudarshan Ragunathan, Laura Bell","Barrow Neurological Institute, USA",BSWleakagecorr,,SR,in-progress -DSC,Parameter derivation,"CBV,CBF,MTT",,SR_TBG_BNI_USAPhoenixUSA,"Sudarshan Ragunathan, Laura Bell","Barrow Neurological Institute, USA",DSCparameters,,tbd, +DSC,Leakage correction,BSW,,SR_TBG_BNI_PhoenixUSA,"Sudarshan Ragunathan, Laura Bell","Barrow Neurological Institute, USA",BSWleakagecorr,,SR,in-progress +DSC,Parameter derivation,"CBV,CBF,MTT",,SR_TBG_BNI_PhoenixUSA,"Sudarshan Ragunathan, Laura Bell","Barrow Neurological Institute, USA",DSCparameters,,tbd, DSC,Signal to deltaR2*,single echo,,LCB_BNI_USA,Laura Bell,"Barrow Neurological Institute, USA",,estimate_delta_R2s,tbd, DSC,Signal to deltaR2*,dual echo,,LCB_BNI_USA,Laura Bell,"Barrow Neurological Institute, USA",,"estimate_delta_R2s, estimate_delta_R2s_dual_echo",tbd, DSC,Signal to R2*,dual echo,,LCB_BNI_USA,Laura Bell,"Barrow Neurological Institute, USA",,estimate_R2s,tbd, \ No newline at end of file diff --git a/notebooks/contributors.ipynb b/notebooks/contributors.ipynb index d8cb90ff..b793223b 100644 --- a/notebooks/contributors.ipynb +++ b/notebooks/contributors.ipynb @@ -947,7 +947,7 @@ " AIF deconvolution\n", " NaN\n", " NaN\n", - " SR_TBG_BNI_USAPhoenixUSA\n", + " SR_TBG_BNI_PhoenixUSA\n", " Sudarshan Ragunathan\n", " Barrow Neurological Institute, USA\n", " tbd\n", @@ -973,7 +973,7 @@ " Leakage correction\n", " BSW\n", " NaN\n", - " SR_TBG_BNI_USAPhoenixUSA\n", + " SR_TBG_BNI_PhoenixUSA\n", " Sudarshan Ragunathan\n", " Barrow Neurological Institute, USA\n", " tbd\n", @@ -1012,7 +1012,7 @@ " Parameter derivation\n", " CBV,CBF,MTT\n", " NaN\n", - " SR_TBG_BNI_USAPhoenixUSA\n", + " SR_TBG_BNI_PhoenixUSA\n", " Sudarshan Ragunathan\n", " Barrow Neurological Institute, USA\n", " tbd\n", @@ -1272,12 +1272,12 @@ "64 linear, nonlinear, two flip angles MJT_UoEdinburghUK \n", "65 two flip angles OG_MO_AUMC_ICR_RMH \n", "66 despot, novifast McGill_VFA \n", - "67 NaN SR_TBG_BNI_USAPhoenixUSA \n", + "67 NaN SR_TBG_BNI_PhoenixUSA \n", "68 fully automatic, semi-automatic JBJA_GUSahlgrenskaSWE \n", - "69 NaN SR_TBG_BNI_USAPhoenixUSA \n", + "69 NaN SR_TBG_BNI_PhoenixUSA \n", "70 NaN LCB_BNI_USA \n", "71 NaN LCB_BNI_USA \n", - "72 NaN SR_TBG_BNI_USAPhoenixUSA \n", + "72 NaN SR_TBG_BNI_PhoenixUSA \n", "73 NaN LCB_BNI_USA \n", "74 NaN LCB_BNI_USA \n", "\n", diff --git a/src/wrappers/tofts.py b/src/wrappers/tofts.py index df11f76c..be3cc6b5 100644 --- a/src/wrappers/tofts.py +++ b/src/wrappers/tofts.py @@ -10,7 +10,7 @@ import osipi_code_collection.original.MJT_UoEdinburghUK.aifs as edinburgh2_aifs import osipi_code_collection.original.MJT_UoEdinburghUK.pk_models as edinburgh2_models import osipi_code_collection.original.MJT_UoEdinburghUK.dce_fit as edinburgh2_fit -import osipi_code_collection.original.OGJ_OsloU_Norway.MRImageAnalysis.DCE.Analyze as oslo +import osipi_code_collection.original.OGJ_OsloU_NOR.MRImageAnalysis.DCE.Analyze as oslo import osipi_code_collection.original.ST_USydAUS.ModelDictionary as sydney from osipi_code_collection.original.MB_QBI_UoManchesterUK.QbiPy.dce_models import dce_aif as manchester_aif from osipi_code_collection.original.MB_QBI_UoManchesterUK.QbiPy.dce_models import tofts_model as manchester_tofts diff --git a/src/wrappers/vfa.py b/src/wrappers/vfa.py index 8ad50656..e72c09c2 100644 --- a/src/wrappers/vfa.py +++ b/src/wrappers/vfa.py @@ -1,6 +1,6 @@ import osipi_code_collection.original.MJT_UoEdinburghUK.t1_fit as edinburgh import osipi_code_collection.original.ST_USydAUS.VFAT1mapping as sydney -import osipi_code_collection.original.McGill_Can.vfa as mcgill +import osipi_code_collection.original.McGill_CAN.vfa as mcgill from osipi_code_collection.utils.nb import percenterror import matplotlib.pyplot as plt import numpy as np diff --git a/test/DCEmodels/test_DCEmodels_tofts_OGJ_OsloU_NOR.py b/test/DCEmodels/test_DCEmodels_tofts_OGJ_OsloU_NOR.py index 5b44b689..6b355724 100644 --- a/test/DCEmodels/test_DCEmodels_tofts_OGJ_OsloU_NOR.py +++ b/test/DCEmodels/test_DCEmodels_tofts_OGJ_OsloU_NOR.py @@ -3,7 +3,7 @@ from time import perf_counter from ..helpers import osipi_parametrize, log_init, log_results from . import DCEmodels_data -from osipi_code_collection.original.OGJ_OsloU_Norway.MRImageAnalysis.DCE.Analyze import fitToModel +from osipi_code_collection.original.OGJ_OsloU_NOR.MRImageAnalysis.DCE.Analyze import fitToModel # All tests will use the same arguments and same data... arg_names = 'label, t_array, C_array, ca_array, ta_array, ve_ref, Ktrans_ref, arterial_delay_ref, a_tol_ve, ' \ diff --git a/test/DSCmodels/test_DSCmodels_LcurveReg_SR_TBG_BNIPhoenixUSA.py b/test/DSCmodels/test_DSCmodels_LcurveReg_SR_TBG_BNIPhoenixUSA.py index db0a9948..fc90fb7c 100644 --- a/test/DSCmodels/test_DSCmodels_LcurveReg_SR_TBG_BNIPhoenixUSA.py +++ b/test/DSCmodels/test_DSCmodels_LcurveReg_SR_TBG_BNIPhoenixUSA.py @@ -3,8 +3,8 @@ from time import perf_counter from ..helpers import osipi_parametrize, log_init, log_results from . import DSCmodels_data -from src.original.SR_TBG_BNI_USAPhoenixUSA.AIFDeconvolution.AIF_deconvolution import AIFdeconvolution -from src.original.SR_TBG_BNI_USAPhoenixUSA.DSCparameters.DSC_parameters import DSCparameters +from src.original.SR_TBG_BNIPhoenixUSA.AIFDeconvolution.AIF_deconvolution import AIFdeconvolution +from src.original.SR_TBG_BNIPhoenixUSA.DSCparameters.DSC_parameters import DSCparameters # All tests will use the same arguments and same data... arg_names = 'label, C_tis, C_aif, tr, cbv_ref, cbf_ref,' \ @@ -25,7 +25,7 @@ def setup_module(module): # Use the test data to generate a parametrize decorator. This causes the following test to be run for every test case # listed in test_data... @osipi_parametrize(arg_names, test_data, xf_labels=[]) -def test_SR_TBG_BNI_USAPhoenixUSA_LcurveReg(label, C_tis, C_aif, tr, cbv_ref, cbf_ref, +def test_SR_TBG_BNI_PhoenixUSA_LcurveReg(label, C_tis, C_aif, tr, cbv_ref, cbf_ref, r_tol_cbv, r_tol_cbf, a_tol_cbv, a_tol_cbf): # run code diff --git a/test/T1_mapping/test_t1_ZA_McGill_CAN.py b/test/T1_mapping/test_t1_ZA_McGill_CAN.py index 0ca8f016..dbb6443b 100644 --- a/test/T1_mapping/test_t1_ZA_McGill_CAN.py +++ b/test/T1_mapping/test_t1_ZA_McGill_CAN.py @@ -4,7 +4,7 @@ from time import perf_counter from ..helpers import osipi_parametrize, log_init, log_results from . import t1_data -from osipi_code_collection.original.McGill_Can.vfa import despot, novifast +from osipi_code_collection.original.ZA_McGill_CAN.vfa import despot, novifast # All tests will use the same arguments and same data... diff --git a/test/results-meta.json b/test/results-meta.json index c71e8c12..1c85efdf 100644 --- a/test/results-meta.json +++ b/test/results-meta.json @@ -4,7 +4,7 @@ "filename": "TestResults_T1mapping_mcgill_t1_VFA_lin.csv", "category": "T1mapping", "method": "linear", - "author": "ZA_McGill_Can" + "author": "ZA_McGill_CAN" }, { "path": "../test/results/T1_mapping", @@ -40,7 +40,7 @@ "filename": "TestResults_T1mapping_mcgill_t1_novifast.csv", "category": "T1mapping", "method": "nonlinear", - "author": "ZA_McGill_Can" + "author": "ZA_McGill_CAN" }, { "path": "../test/results/T1_mapping", From a913134568b20e30d1c46b7fe646c71442d5faed Mon Sep 17 00:00:00 2001 From: mjt320 Date: Wed, 31 Aug 2022 15:38:39 +0100 Subject: [PATCH 9/9] naming --- doc/code_contributions_record.csv | 66 ++++++------ notebooks/contributors.ipynb | 96 +++++++++--------- .../AIF_selection_automatic.py | 0 .../AIF_selection_auto/__init__.py | 0 .../demo/auto_AIF_result_fig.jpeg | Bin .../demo/auto_AIF_result_fig_Mouridsen.jpeg | Bin .../data/4d_concentration_masked_anon.nii.gz | Bin .../demo/data/MCAsin_anon.nii | Bin .../demo/data/brain_mask_3d_anon.nii.gz | Bin .../demo/data/test_artery_ROI.nii | Bin .../demo/data/test_concentration.nii | Bin .../AIF_selection_auto/demo/demo.ipynb | 0 .../AIF_selection_auto/demo/plots.py | 0 .../AIF_selection_auto/plots.py | 0 .../BAT_estimation.py | 0 .../PharmacokineticModelling/__init__.py | 0 .../PharmacokineticModelling/models.py | 0 .../SignalToConcentration/SI2Conc.py | 0 .../SignalToConcentration/__init__.py | 0 .../__init__.py | 0 .../QbiPy/README.md | 0 .../QbiPy/__init__.py | 0 .../QbiPy/dce_models/__init__.py | 0 .../QbiPy/dce_models/active_uptake_model.py | 0 .../QbiPy/dce_models/dce_aif.py | 0 .../QbiPy/dce_models/dibem.py | 0 .../QbiPy/dce_models/tissue_concentration.py | 0 .../QbiPy/dce_models/tofts_model.py | 0 .../QbiPy/dce_models/two_cfm_model.py | 0 .../QbiPy/dce_models/two_cxm_model.py | 0 .../QbiPy/examples/tofts_model_example.py | 0 .../QbiPy/helpers.py | 0 .../QbiPy/t1_mapping/VFA.py | 0 .../QbiPy/t1_mapping/__init__.py | 0 .../__init__.py | 0 .../README.md | 0 .../__init__.py | 0 .../aifs.py | 0 .../dce_fit.py | 0 .../fitting.py | 0 .../pk_models.py | 0 .../relaxivity.py | 0 .../signal_models.py | 0 .../t1_fit.py | 0 .../utils/__init__.py | 0 .../utils/imaging.py | 0 .../utils/utilities.py | 0 .../water_ex_models.py | 0 .../AIFDeconvolution/AIF_deconvolution.py | 0 .../AIFDeconvolution/__init__.py | 0 .../DSCparameters/DSC_parameters.py | 0 .../DSCparameters/__init__.py | 0 .../LeakageCorrection/__init__.py | 0 .../LeakageCorrection/bsw_leakagecorr.py | 0 .../LeakageCorrection/requirements.txt | 0 .../__init__.py | 0 .../InputFunctions.py | 0 .../ModelDictionary.py | 0 .../{ST_USydAUS => ST_USyd_AUS}/Tools.py | 0 .../VFAT1mapping.py | 0 .../{ST_USydAUS => ST_USyd_AUS}/__init__.py | 0 .../signals2conc.py | 0 src/wrappers/tofts.py | 12 +-- src/wrappers/vfa.py | 2 +- ...test_DCEmodels_2CUM_LEK_UoEdinburgh_UK.py} | 12 +-- ...test_DCEmodels_2CUM_MJT_UoEdinburgh_UK.py} | 12 +-- ...test_DCEmodels_2CXM_LEK_UoEdinburgh_UK.py} | 12 +-- ..._DCEmodels_2CXM_MB_QBI_UoManchester_UK.py} | 8 +- ...test_DCEmodels_2CXM_MJT_UoEdinburgh_UK.py} | 12 +-- .../test_DCEmodels_2CXM_OGJ_OsloU_NOR.py | 2 +- ...st_DCEmodels_Patlak_LEK_UoEdinburgh_UK.py} | 12 +-- ...st_DCEmodels_Patlak_MJT_UoEdinburgh_UK.py} | 18 ++-- ...y => test_DCEmodels_Patlak_ST_USyd_AUS.py} | 7 +- ...st_DCEmodels_etofts_LEK_UoEdinburgh_UK.py} | 12 +-- ...CEmodels_etofts_MB_QBI_UoManchester_UK.py} | 2 +- ...st_DCEmodels_etofts_MJT_UoEdinburgh_UK.py} | 12 +-- .../test_DCEmodels_etofts_OGJ_OsloU_NOR.py | 10 +- ...Emodels_etofts_OG_MO_AUMC_ICR_RMH_NL_UK.py | 9 +- ...y => test_DCEmodels_etofts_ST_USyd_AUS.py} | 5 +- ...est_DCEmodels_tofts_LEK_UoEdinburgh_UK.py} | 12 +-- ...est_DCEmodels_tofts_MJT_UoEdinburgh_UK.py} | 12 +-- .../test_DCEmodels_tofts_OGJ_OsloU_NOR.py | 10 +- ...py => test_DCEmodels_tofts_ST_USyd_AUS.py} | 5 +- ...models_LcurveReg_SR_TBG_BNIPhoenix_USA.py} | 4 +- ...t_popAIF_Parker_MB_QBI_UoManchester_UK.py} | 8 +- ...=> test_popAIF_Parker_MJT_Edinburgh_UK.py} | 8 +- ...py => test_popAIF_Parker_ST_Sydney_AUS.py} | 7 +- ... test_popAIF_preclinical_ST_Sydney_AUS.py} | 6 +- ...UK.py => test_SI2Conc_LEK_Edinburgh_UK.py} | 4 +- ...=> test_SI2Conc_MB_QBI_UoManchester_UK.py} | 2 +- ....py => test_SI2Conc_MJT_UoEdinburgh_UK.py} | 12 +-- .../test_SI2Conc_OG_MO_AUMC_ICR_RMH_NL_UK.py | 5 +- ...USydAUS.py => test_SI2Conc_ST_USyd_AUS.py} | 5 +- ...burghUK.py => test_t1_MJT_Edinburgh_UK.py} | 20 ++-- .../test_t1_OG_MO_AUMC_ICR_RMH_NL_UK.py | 12 ++- ..._SydneyAUS.py => test_t1_ST_Sydney_AUS.py} | 16 +-- test/T1_mapping/test_t1_ZA_McGill_CAN.py | 7 +- test/results-meta.json | 44 ++++---- 98 files changed, 271 insertions(+), 249 deletions(-) rename src/original/{JBJA_GUSahlgrenskaSWE => JBJA_GUSahlgrenska_SWE}/AIF_selection_auto/AIF_selection_automatic.py (100%) rename src/original/{JBJA_GUSahlgrenskaSWE => JBJA_GUSahlgrenska_SWE}/AIF_selection_auto/__init__.py (100%) rename src/original/{JBJA_GUSahlgrenskaSWE => JBJA_GUSahlgrenska_SWE}/AIF_selection_auto/demo/auto_AIF_result_fig.jpeg (100%) rename src/original/{JBJA_GUSahlgrenskaSWE => JBJA_GUSahlgrenska_SWE}/AIF_selection_auto/demo/auto_AIF_result_fig_Mouridsen.jpeg (100%) rename src/original/{JBJA_GUSahlgrenskaSWE => JBJA_GUSahlgrenska_SWE}/AIF_selection_auto/demo/data/4d_concentration_masked_anon.nii.gz (100%) rename src/original/{JBJA_GUSahlgrenskaSWE => JBJA_GUSahlgrenska_SWE}/AIF_selection_auto/demo/data/MCAsin_anon.nii (100%) rename src/original/{JBJA_GUSahlgrenskaSWE => JBJA_GUSahlgrenska_SWE}/AIF_selection_auto/demo/data/brain_mask_3d_anon.nii.gz (100%) rename src/original/{JBJA_GUSahlgrenskaSWE => JBJA_GUSahlgrenska_SWE}/AIF_selection_auto/demo/data/test_artery_ROI.nii (100%) rename src/original/{JBJA_GUSahlgrenskaSWE => JBJA_GUSahlgrenska_SWE}/AIF_selection_auto/demo/data/test_concentration.nii (100%) rename src/original/{JBJA_GUSahlgrenskaSWE => JBJA_GUSahlgrenska_SWE}/AIF_selection_auto/demo/demo.ipynb (100%) rename src/original/{JBJA_GUSahlgrenskaSWE => JBJA_GUSahlgrenska_SWE}/AIF_selection_auto/demo/plots.py (100%) rename src/original/{JBJA_GUSahlgrenskaSWE => JBJA_GUSahlgrenska_SWE}/AIF_selection_auto/plots.py (100%) rename src/original/{LEK_UoEdinburghUK => LEK_UoEdinburgh_UK}/PharmacokineticModelling/BAT_estimation.py (100%) rename src/original/{LEK_UoEdinburghUK => LEK_UoEdinburgh_UK}/PharmacokineticModelling/__init__.py (100%) rename src/original/{LEK_UoEdinburghUK => LEK_UoEdinburgh_UK}/PharmacokineticModelling/models.py (100%) rename src/original/{LEK_UoEdinburghUK => LEK_UoEdinburgh_UK}/SignalToConcentration/SI2Conc.py (100%) rename src/original/{LEK_UoEdinburghUK => LEK_UoEdinburgh_UK}/SignalToConcentration/__init__.py (100%) rename src/original/{LEK_UoEdinburghUK => LEK_UoEdinburgh_UK}/__init__.py (100%) rename src/original/{MB_QBI_UoManchesterUK => MB_QBI_UoManchester_UK}/QbiPy/README.md (100%) rename src/original/{MB_QBI_UoManchesterUK => MB_QBI_UoManchester_UK}/QbiPy/__init__.py (100%) rename src/original/{MB_QBI_UoManchesterUK => MB_QBI_UoManchester_UK}/QbiPy/dce_models/__init__.py (100%) rename src/original/{MB_QBI_UoManchesterUK => MB_QBI_UoManchester_UK}/QbiPy/dce_models/active_uptake_model.py (100%) rename src/original/{MB_QBI_UoManchesterUK => MB_QBI_UoManchester_UK}/QbiPy/dce_models/dce_aif.py (100%) rename src/original/{MB_QBI_UoManchesterUK => MB_QBI_UoManchester_UK}/QbiPy/dce_models/dibem.py (100%) rename src/original/{MB_QBI_UoManchesterUK => MB_QBI_UoManchester_UK}/QbiPy/dce_models/tissue_concentration.py (100%) rename src/original/{MB_QBI_UoManchesterUK => MB_QBI_UoManchester_UK}/QbiPy/dce_models/tofts_model.py (100%) rename src/original/{MB_QBI_UoManchesterUK => MB_QBI_UoManchester_UK}/QbiPy/dce_models/two_cfm_model.py (100%) rename src/original/{MB_QBI_UoManchesterUK => MB_QBI_UoManchester_UK}/QbiPy/dce_models/two_cxm_model.py (100%) rename src/original/{MB_QBI_UoManchesterUK => MB_QBI_UoManchester_UK}/QbiPy/examples/tofts_model_example.py (100%) rename src/original/{MB_QBI_UoManchesterUK => MB_QBI_UoManchester_UK}/QbiPy/helpers.py (100%) rename src/original/{MB_QBI_UoManchesterUK => MB_QBI_UoManchester_UK}/QbiPy/t1_mapping/VFA.py (100%) rename src/original/{MB_QBI_UoManchesterUK => MB_QBI_UoManchester_UK}/QbiPy/t1_mapping/__init__.py (100%) rename src/original/{MB_QBI_UoManchesterUK => MB_QBI_UoManchester_UK}/__init__.py (100%) rename src/original/{MJT_UoEdinburghUK => MJT_UoEdinburgh_UK}/README.md (100%) rename src/original/{MJT_UoEdinburghUK => MJT_UoEdinburgh_UK}/__init__.py (100%) rename src/original/{MJT_UoEdinburghUK => MJT_UoEdinburgh_UK}/aifs.py (100%) rename src/original/{MJT_UoEdinburghUK => MJT_UoEdinburgh_UK}/dce_fit.py (100%) rename src/original/{MJT_UoEdinburghUK => MJT_UoEdinburgh_UK}/fitting.py (100%) rename src/original/{MJT_UoEdinburghUK => MJT_UoEdinburgh_UK}/pk_models.py (100%) rename src/original/{MJT_UoEdinburghUK => MJT_UoEdinburgh_UK}/relaxivity.py (100%) rename src/original/{MJT_UoEdinburghUK => MJT_UoEdinburgh_UK}/signal_models.py (100%) rename src/original/{MJT_UoEdinburghUK => MJT_UoEdinburgh_UK}/t1_fit.py (100%) rename src/original/{MJT_UoEdinburghUK => MJT_UoEdinburgh_UK}/utils/__init__.py (100%) rename src/original/{MJT_UoEdinburghUK => MJT_UoEdinburgh_UK}/utils/imaging.py (100%) rename src/original/{MJT_UoEdinburghUK => MJT_UoEdinburgh_UK}/utils/utilities.py (100%) rename src/original/{MJT_UoEdinburghUK => MJT_UoEdinburgh_UK}/water_ex_models.py (100%) rename src/original/{SR_TBG_BNIPhoenixUSA => SR_TBG_BNIPhoenix_USA}/AIFDeconvolution/AIF_deconvolution.py (100%) rename src/original/{SR_TBG_BNIPhoenixUSA => SR_TBG_BNIPhoenix_USA}/AIFDeconvolution/__init__.py (100%) rename src/original/{SR_TBG_BNIPhoenixUSA => SR_TBG_BNIPhoenix_USA}/DSCparameters/DSC_parameters.py (100%) rename src/original/{SR_TBG_BNIPhoenixUSA => SR_TBG_BNIPhoenix_USA}/DSCparameters/__init__.py (100%) rename src/original/{SR_TBG_BNIPhoenixUSA => SR_TBG_BNIPhoenix_USA}/LeakageCorrection/__init__.py (100%) rename src/original/{SR_TBG_BNIPhoenixUSA => SR_TBG_BNIPhoenix_USA}/LeakageCorrection/bsw_leakagecorr.py (100%) rename src/original/{SR_TBG_BNIPhoenixUSA => SR_TBG_BNIPhoenix_USA}/LeakageCorrection/requirements.txt (100%) rename src/original/{SR_TBG_BNIPhoenixUSA => SR_TBG_BNIPhoenix_USA}/__init__.py (100%) rename src/original/{ST_USydAUS => ST_USyd_AUS}/InputFunctions.py (100%) rename src/original/{ST_USydAUS => ST_USyd_AUS}/ModelDictionary.py (100%) rename src/original/{ST_USydAUS => ST_USyd_AUS}/Tools.py (100%) rename src/original/{ST_USydAUS => ST_USyd_AUS}/VFAT1mapping.py (100%) rename src/original/{ST_USydAUS => ST_USyd_AUS}/__init__.py (100%) rename src/original/{ST_USydAUS => ST_USyd_AUS}/signals2conc.py (100%) rename test/DCEmodels/{test_DCEmodels_2CUM_LEK_UoEdinburghUK.py => test_DCEmodels_2CUM_LEK_UoEdinburgh_UK.py} (92%) rename test/DCEmodels/{test_DCEmodels_2CUM_MJT_UoEdinburghUK.py => test_DCEmodels_2CUM_MJT_UoEdinburgh_UK.py} (87%) rename test/DCEmodels/{test_DCEmodels_2CXM_LEK_UoEdinburghUK.py => test_DCEmodels_2CXM_LEK_UoEdinburgh_UK.py} (92%) rename test/DCEmodels/{test_DCEmodels_2CXM_MB_QBI_UoManchesterUK.py => test_DCEmodels_2CXM_MB_QBI_UoManchester_UK.py} (86%) rename test/DCEmodels/{test_DCEmodels_2CXM_MJT_UoEdinburghUK.py => test_DCEmodels_2CXM_MJT_UoEdinburgh_UK.py} (91%) rename test/DCEmodels/{test_DCEmodels_Patlak_LEK_UoEdinburghUK.py => test_DCEmodels_Patlak_LEK_UoEdinburgh_UK.py} (88%) rename test/DCEmodels/{test_DCEmodels_Patlak_MJT_UoEdinburghUK.py => test_DCEmodels_Patlak_MJT_UoEdinburgh_UK.py} (84%) rename test/DCEmodels/{test_DCEmodels_Patlak_ST_USydAUS.py => test_DCEmodels_Patlak_ST_USyd_AUS.py} (87%) rename test/DCEmodels/{test_DCEmodels_etofts_LEK_UoEdinburghUK.py => test_DCEmodels_etofts_LEK_UoEdinburgh_UK.py} (81%) rename test/DCEmodels/{test_DCEmodels_etofts_MB_QBI_UoManchesterUK.py => test_DCEmodels_etofts_MB_QBI_UoManchester_UK.py} (95%) rename test/DCEmodels/{test_DCEmodels_etofts_MJT_UoEdinburghUK.py => test_DCEmodels_etofts_MJT_UoEdinburgh_UK.py} (83%) rename test/DCEmodels/{test_DCEmodels_etofts_ST_USydAUS.py => test_DCEmodels_etofts_ST_USyd_AUS.py} (90%) rename test/DCEmodels/{test_DCEmodels_tofts_LEK_UoEdinburghUK.py => test_DCEmodels_tofts_LEK_UoEdinburgh_UK.py} (85%) rename test/DCEmodels/{test_DCEmodels_tofts_MJT_UoEdinburghUK.py => test_DCEmodels_tofts_MJT_UoEdinburgh_UK.py} (82%) rename test/DCEmodels/{test_DCEmodels_tofts_ST_USydAUS.py => test_DCEmodels_tofts_ST_USyd_AUS.py} (89%) rename test/DSCmodels/{test_DSCmodels_LcurveReg_SR_TBG_BNIPhoenixUSA.py => test_DSCmodels_LcurveReg_SR_TBG_BNIPhoenix_USA.py} (90%) rename test/PopulationAIF_DCE/{test_popAIF_Parker_MB_QBI_UoManchesterUK.py => test_popAIF_Parker_MB_QBI_UoManchester_UK.py} (85%) rename test/PopulationAIF_DCE/{test_popAIF_Parker_MJT_EdinburghUK.py => test_popAIF_Parker_MJT_Edinburgh_UK.py} (82%) rename test/PopulationAIF_DCE/{test_popAIF_Parker_ST_SydneyAUS.py => test_popAIF_Parker_ST_Sydney_AUS.py} (84%) rename test/PopulationAIF_DCE/{test_popAIF_preclinical_ST_SydneyAUS.py => test_popAIF_preclinical_ST_Sydney_AUS.py} (84%) rename test/SI_to_Conc/{test_SI2Conc_LEK_EdinburghUK.py => test_SI2Conc_LEK_Edinburgh_UK.py} (89%) mode change 100755 => 100644 rename test/SI_to_Conc/{test_SI2Conc_MB_QBI_UoManchesterUK.py => test_SI2Conc_MB_QBI_UoManchester_UK.py} (94%) rename test/SI_to_Conc/{test_SI2Conc_MJT_UoEdinburghUK.py => test_SI2Conc_MJT_UoEdinburgh_UK.py} (86%) rename test/SI_to_Conc/{test_SI2Conc_ST_USydAUS.py => test_SI2Conc_ST_USyd_AUS.py} (90%) rename test/T1_mapping/{test_t1_MJT_EdinburghUK.py => test_t1_MJT_Edinburgh_UK.py} (68%) rename test/T1_mapping/{test_t1_ST_SydneyAUS.py => test_t1_ST_Sydney_AUS.py} (72%) diff --git a/doc/code_contributions_record.csv b/doc/code_contributions_record.csv index 7e85457a..104c0e96 100644 --- a/doc/code_contributions_record.csv +++ b/doc/code_contributions_record.csv @@ -1,12 +1,12 @@ Technique,Category,Subcategory,Notes,Subfolder,Authors,Institution,function/module name,doi,Tester,Test status (empty/in-progress/complete) DCE,Bolus arrival time,piecewise linear quadratic function,Cheong et al (DOI: 10.1088/0031-9155/48/5/403),LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",BAT_linquad,,tbd, DCE,Bolus arrival time,fitting Kety (Tofts) model to first third of the curve,,LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",BAT_kety,,tbd, -DCE,Input Functions,load AIF,load from txt,MB_QBI_UoManchesterUK,Michael Berks,"University of Manchester, UK",read_AIF,https://doi.org/10.21105/joss.03523,tbd, -DCE,Input Functions,Parker AIF,,MB_QBI_UoManchesterUK,Michael Berks,"University of Manchester, UK",compute_population_AIF,https://doi.org/10.21105/joss.03523,JK/PvH,completed -DCE,Input Functions,patient-specific AIF,constructed from time-concentration data,MJT_UoEdinburghUK,Michael Thrippleton,"University of Edinburgh, UK",patientSpecific,,tbd, -DCE,Input Functions,Parker AIF,"Parker AIF, Parker-like AIF",MJT_UoEdinburghUK,Michael Thrippleton,"University of Edinburgh, UK",Parker,,JK/PvH,completed -DCE,Input Functions,Manning AIF,Manning et al (https://doi.org/10.1002/mrm.28833),MJT_UoEdinburghUK,Michael Thrippleton,"University of Edinburgh, UK","ManningFast, ManningSlow",,tbd,completed -DCE,Input Functions,Heye AIF,Heye et al (https://doi.org/10.1016/j.neuroimage.2015.10.018),MJT_UoEdinburghUK,Michael Thrippleton,"University of Edinburgh, UK",Heye,,tbd,completed +DCE,Input Functions,load AIF,load from txt,MB_QBI_UoManchester_UK,Michael Berks,"University of Manchester, UK",read_AIF,https://doi.org/10.21105/joss.03523,tbd, +DCE,Input Functions,Parker AIF,,MB_QBI_UoManchester_UK,Michael Berks,"University of Manchester, UK",compute_population_AIF,https://doi.org/10.21105/joss.03523,JK/PvH,completed +DCE,Input Functions,patient-specific AIF,constructed from time-concentration data,MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK",patientSpecific,,tbd, +DCE,Input Functions,Parker AIF,"Parker AIF, Parker-like AIF",MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK",Parker,,JK/PvH,completed +DCE,Input Functions,Manning AIF,Manning et al (https://doi.org/10.1002/mrm.28833),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","ManningFast, ManningSlow",,tbd,completed +DCE,Input Functions,Heye AIF,Heye et al (https://doi.org/10.1016/j.neuroimage.2015.10.018),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK",Heye,,tbd,completed DCE,Input Functions,AIF parameterization,,OG_MO_AUMC_ICR_RMH,"Oliver Gurney-Champion, Matthew Orton","Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK","Cosine4AIF, Cosine8AIF",https://doi.org/10.1088/0031-9155/53/5/005; https://doi.org/10.1007/s00330-015-4012-9,tbd, DCE,Input Functions,Head-and-neck population AIF,Wong et al (DOI: https://doi.org/10.2967/jnumed.116.174433),OG_MO_AUMC_ICR_RMH,"Oliver Gurney-Champion, Matthew Orton","Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK",aifPopHN,,tbd, DCE,Input Functions,Parker AIF,,OG_MO_AUMC_ICR_RMH,"Oliver Gurney-Champion, Matthew Orton","Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK",aifPopPMB,,tbd, @@ -17,7 +17,7 @@ DCE,Input Functions,Parker AIF,,PvH_NKI,Petra van Houdt,"the Netherlands Cancer DCE,Input Functions,Parker AIF,,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia","AIF, variableAIF",,JK/PvH,completed DCE,Input Functions,preclinical AIF,McGrath et al (DOI: 10.1002/mrm.21959),ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",preclinicalAIF,,JK/PvH,completed DCE,Miscellaneous,enhancement detection,check for enhancement,OG_MO_AUMC_ICR_RMH,"Oliver Gurney-Champion, Matthew Orton","Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK",enhance,,tbd, -DCE,Parameter derivation,iAUC,,MB_QBI_UoManchesterUK,Michael Berks,"University of Manchester, UK",compute_IAUC,https://doi.org/10.21105/joss.03523,tbd, +DCE,Parameter derivation,iAUC,,MB_QBI_UoManchester_UK,Michael Berks,"University of Manchester, UK",compute_IAUC,https://doi.org/10.21105/joss.03523,tbd, DCE,Pharmacokinetic models,Tofts,NLLS fitting (+forward model),DS_BW_VanderBiltUMC_USA,"David Smith, Brian Welch","VanderBilt University Medical Center, USA","tofts_integral, fit_tofts_model",,tdd, DCE,Pharmacokinetic models,extended Tofts,NLLS fitting (+forward model),DS_BW_VanderBiltUMC_USA,"David Smith, Brian Welch","VanderBilt University Medical Center, USA","ext_tofts_integral, fit_tofts_model",,tbd, DCE,Pharmacokinetic models,Tofts,NLLS fitting (+ forward model),LCB_BNI_USA,Laura Bell,"Barrow Neurological Institute, USA","tofts_model, fit_tofts",,ST/OGC,completed @@ -27,24 +27,24 @@ DCE,Pharmacokinetic models,AATH,forward model,LEK_UoEdinburgh,Lucy Kershaw,"Univ DCE,Pharmacokinetic models,extended Tofts,forward model,LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",ExtKety,,ST/OGC,completed DCE,Pharmacokinetic models,Patlak,forward model,LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",Patlak,,MJT,completed DCE,Pharmacokinetic models,Tofts,forward model,LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",Kety,,ST/OGC,completed -DCE,Pharmacokinetic models,2-cmp exchange,LLSQ fitting (+forward model),MB_QBI_UoManchesterUK,Michael Berks,"University of Manchester, UK",two_cxm_model,https://doi.org/10.21105/joss.03523,MJT,completed -DCE,Pharmacokinetic models,2-cmp filtration,LLSQ fitting (+forward model),MB_QBI_UoManchesterUK,Michael Berks,"University of Manchester, UK",two_cfm_model,https://doi.org/10.21105/joss.03523,tbd, -DCE,Pharmacokinetic models,active uptake and efflux (AUEM),LLSQ fitting (+forward model),MB_QBI_UoManchesterUK,Michael Berks,"University of Manchester, UK",active_uptake_model,https://doi.org/10.21105/joss.03523,tbd, -DCE,Pharmacokinetic models,dual-inlet general model,LLSQ fitting (+forward model),MB_QBI_UoManchesterUK,Michael Berks,"University of Manchester, UK",dibem,https://doi.org/10.21105/joss.03523,tbd, -DCE,Pharmacokinetic models,extended Tofts,LLSQ fitting (+forward model),MB_QBI_UoManchesterUK,Michael Berks,"University of Manchester, UK",tofts_model,https://doi.org/10.21105/joss.03523,ST/OGC,completed -DCE,Pharmacokinetic models,2-cmp exchange,NLLS fitting to concentration values (incl forward model),MJT_UoEdinburghUK,Michael Thrippleton,"University of Edinburgh, UK","TCXM, EnhToPKP, ConcToPKP",,MJT,completed -DCE,Pharmacokinetic models,2-cmp exchange,NLLS fitting to signal incl. water exchange (incl forward model),MJT_UoEdinburghUK,Michael Thrippleton,"University of Edinburgh, UK","TCXM, EnhToPKP, ConcToPKP",,MJT,completed -DCE,Pharmacokinetic models,2-cmp uptake,NLLS fitting to concentration values (incl forward model),MJT_UoEdinburghUK,Michael Thrippleton,"University of Edinburgh, UK","TCUM, EnhToPKP, ConcToPKP",,MJT,completed -DCE,Pharmacokinetic models,2-cmp uptake,NLLS fitting to signal incl. water exchange (incl forward model),MJT_UoEdinburghUK,Michael Thrippleton,"University of Edinburgh, UK","TCUM, EnhToPKP, ConcToPKP",,MJT,completed -DCE,Pharmacokinetic models,extended Tofts,NLLS fitting to concentration values (incl forward model),MJT_UoEdinburghUK,Michael Thrippleton,"University of Edinburgh, UK","ExtendedTofts, EnhToPKP, ConcToPKP",,ST/OGC,completed -DCE,Pharmacokinetic models,extended Tofts,NLLS fitting to signal incl. water exchange (incl forward model),MJT_UoEdinburghUK,Michael Thrippleton,"University of Edinburgh, UK","ExtendedTofts, EnhToPKP, ConcToPKP",,ST/OGC,completed -DCE,Pharmacokinetic models,Patlak,NLLS fitting to concentration values (incl forward model),MJT_UoEdinburghUK,Michael Thrippleton,"University of Edinburgh, UK","Patlak, EnhToPKP, ConcToPKP",,MJT,completed -DCE,Pharmacokinetic models,Patlak,NLLS fitting to signal incl. water exchange (incl forward model),MJT_UoEdinburghUK,Michael Thrippleton,"University of Edinburgh, UK","Patlak, EnhToPKP, ConcToPKP",,MJT,completed -DCE,Pharmacokinetic models,Patlak,LLSQ fitting,MJT_UoEdinburghUK,Michael Thrippleton,"University of Edinburgh, UK",PatlakLinear,,MJT,completed -DCE,Pharmacokinetic models,steady-state vp,NLLS fitting to concentration values (incl forward model),MJT_UoEdinburghUK,Michael Thrippleton,"University of Edinburgh, UK","SteadyStateVp, EnhToPKP, ConcToPKP",,tbd, -DCE,Pharmacokinetic models,steady-state vp,NLLS fitting to signal incl. water exchange (incl forward model),MJT_UoEdinburghUK,Michael Thrippleton,"University of Edinburgh, UK","SteadyStateVp, EnhToPKP, ConcToPKP",,tbd, -DCE,Pharmacokinetic models,Tofts,NLLS fitting to concentration values (incl forward model),MJT_UoEdinburghUK,Michael Thrippleton,"University of Edinburgh, UK","Tofts, EnhToPKP, ConcToPKP",,ST/OGC,completed -DCE,Pharmacokinetic models,Tofts,NLLS fitting to signal incl. water exchange (incl forward model),MJT_UoEdinburghUK,Michael Thrippleton,"University of Edinburgh, UK","Tofts,EnhToPKP, ConcToPKP",,ST/OGC,completed +DCE,Pharmacokinetic models,2-cmp exchange,LLSQ fitting (+forward model),MB_QBI_UoManchester_UK,Michael Berks,"University of Manchester, UK",two_cxm_model,https://doi.org/10.21105/joss.03523,MJT,completed +DCE,Pharmacokinetic models,2-cmp filtration,LLSQ fitting (+forward model),MB_QBI_UoManchester_UK,Michael Berks,"University of Manchester, UK",two_cfm_model,https://doi.org/10.21105/joss.03523,tbd, +DCE,Pharmacokinetic models,active uptake and efflux (AUEM),LLSQ fitting (+forward model),MB_QBI_UoManchester_UK,Michael Berks,"University of Manchester, UK",active_uptake_model,https://doi.org/10.21105/joss.03523,tbd, +DCE,Pharmacokinetic models,dual-inlet general model,LLSQ fitting (+forward model),MB_QBI_UoManchester_UK,Michael Berks,"University of Manchester, UK",dibem,https://doi.org/10.21105/joss.03523,tbd, +DCE,Pharmacokinetic models,extended Tofts,LLSQ fitting (+forward model),MB_QBI_UoManchester_UK,Michael Berks,"University of Manchester, UK",tofts_model,https://doi.org/10.21105/joss.03523,ST/OGC,completed +DCE,Pharmacokinetic models,2-cmp exchange,NLLS fitting to concentration values (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","TCXM, EnhToPKP, ConcToPKP",,MJT,completed +DCE,Pharmacokinetic models,2-cmp exchange,NLLS fitting to signal incl. water exchange (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","TCXM, EnhToPKP, ConcToPKP",,MJT,completed +DCE,Pharmacokinetic models,2-cmp uptake,NLLS fitting to concentration values (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","TCUM, EnhToPKP, ConcToPKP",,MJT,completed +DCE,Pharmacokinetic models,2-cmp uptake,NLLS fitting to signal incl. water exchange (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","TCUM, EnhToPKP, ConcToPKP",,MJT,completed +DCE,Pharmacokinetic models,extended Tofts,NLLS fitting to concentration values (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","ExtendedTofts, EnhToPKP, ConcToPKP",,ST/OGC,completed +DCE,Pharmacokinetic models,extended Tofts,NLLS fitting to signal incl. water exchange (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","ExtendedTofts, EnhToPKP, ConcToPKP",,ST/OGC,completed +DCE,Pharmacokinetic models,Patlak,NLLS fitting to concentration values (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","Patlak, EnhToPKP, ConcToPKP",,MJT,completed +DCE,Pharmacokinetic models,Patlak,NLLS fitting to signal incl. water exchange (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","Patlak, EnhToPKP, ConcToPKP",,MJT,completed +DCE,Pharmacokinetic models,Patlak,LLSQ fitting,MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK",PatlakLinear,,MJT,completed +DCE,Pharmacokinetic models,steady-state vp,NLLS fitting to concentration values (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","SteadyStateVp, EnhToPKP, ConcToPKP",,tbd, +DCE,Pharmacokinetic models,steady-state vp,NLLS fitting to signal incl. water exchange (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","SteadyStateVp, EnhToPKP, ConcToPKP",,tbd, +DCE,Pharmacokinetic models,Tofts,NLLS fitting to concentration values (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","Tofts, EnhToPKP, ConcToPKP",,ST/OGC,completed +DCE,Pharmacokinetic models,Tofts,NLLS fitting to signal incl. water exchange (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","Tofts,EnhToPKP, ConcToPKP",,ST/OGC,completed DCE,Pharmacokinetic models,extended Tofts,NLLS fitting (+forward model),OG_MO_AUMC_ICR_RMH,"Oliver Gurney-Champion, Matthew Orton","Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK",fit_tofts_model,,ST/OGC,completed DCE,Pharmacokinetic models,2-cmp exchange,LLSQ fitting (+ forward model),OGJ_OsloU_NOR,Ole Gunnar Johansen,"University of Oslo, Norway","twoCXM, fitToModelLLSQ",,MJT,completed DCE,Pharmacokinetic models,extended Tofts,NLLS fitting (+ forward model),OGJ_OsloU_NOR,Ole Gunnar Johansen,"University of Oslo, Norway","ETM, fitToModelNLLS, fitToModelNLLS_parallel",,ST/OGC,completed @@ -62,21 +62,21 @@ DCE,Pharmacokinetic models,Patlak,forward model,ST_USydAUS_DCE,Sirisha Tadimalla DCE,Signal to Concentration,SPGR,"two-steps: S->R1, R1->C",DS_BW_VanderBiltUMC_USA,"David Smith, Brian Welch","VanderBilt University Medical Center, USA","r1eff_to_conc, dce_to_r1eff",,tbd, DCE,Signal to Concentration,SPGR or GE-EPI,,LCB_BNI_USA,Laura Bell,"Barrow Neurological Institute, USA","signal_to_conc, estimate_delta_R1",,LK,completed DCE,Signal to concentration,SPGR,"reverse C->S also available",LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",SI2Conc,,LK,completed -DCE,Signal to concentration,SPGR,"reverse C->S also available",MB_QBI_UoManchesterUK,Michael Berks,"University of Manchester, UK",signal_to_concentration,https://doi.org/10.21105/joss.03523,LK,completed -DCE,Signal to concentration,SPGR,"two steps: S-> enhancement, enhancement -> C; reverse C->S also available",MJT_UoEdinburghUK,Michael Thrippleton,"University of Edinburgh, UK","sign_to_enh, enh_to_conc",,LK,completed +DCE,Signal to concentration,SPGR,"reverse C->S also available",MB_QBI_UoManchester_UK,Michael Berks,"University of Manchester, UK",signal_to_concentration,https://doi.org/10.21105/joss.03523,LK,completed +DCE,Signal to concentration,SPGR,"two steps: S-> enhancement, enhancement -> C; reverse C->S also available",MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","sign_to_enh, enh_to_conc",,LK,completed DCE,Signal to concentration,SPGR,"two steps: S->R1, R1 -> C; reverse C->S also available",OG_MO_AUMC_ICR_RMH,"Oliver Gurney-Champion, Matthew Orton","Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK","dce_to_r1eff, r1eff_to_conc",,LK,completed DCE,Signal to concentration,SPGR,"reverse R1->C also available",ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",signals2conc,,LK,completed DCE,T1,VFA,nonlinear,DS_BW_VanderBiltUMC_USA,"David Smith, Brian Welch","VanderBilt University Medical Center, USA",fit_R1,,tbd, DCE,T1,VFA,despot,McGill_VFA,Zaki Ahmed,"McGill University, Canada",despot,,MJT,completed DCE,T1,VFA,novifast,McGill_VFA,Zaki Ahmed,"McGill University, Canada",novifast,,MJT,completed -DCE,T1,DESPOT1-HIFI,Fit any combination of (IR-)SPGR scans to estimate T1,MJT_UoEdinburghUK,Michael Thrippleton,"University of Edinburgh, UK",HIFI,,MJT,in-progress -DCE,T1,VFA,linear,MJT_UoEdinburghUK,Michael Thrippleton,"University of Edinburgh, UK",VFALinear,,MJT,complete -DCE,T1,VFA,nonlinear,MJT_UoEdinburghUK,Michael Thrippleton,"University of Edinburgh, UK",VFANonlinear,,MJT,complete -DCE,T1,VFA,two flip angles,MJT_UoEdinburghUK,Michael Thrippleton,"University of Edinburgh, UK",VFA2Points,,tbd, +DCE,T1,DESPOT1-HIFI,Fit any combination of (IR-)SPGR scans to estimate T1,MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK",HIFI,,MJT,in-progress +DCE,T1,VFA,linear,MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK",VFALinear,,MJT,complete +DCE,T1,VFA,nonlinear,MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK",VFANonlinear,,MJT,complete +DCE,T1,VFA,two flip angles,MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK",VFA2Points,,tbd, DCE,T1,VFA,two flip angles (linear),OG_MO_AUMC_ICR_RMH,"Oliver Gurney-Champion, Matthew Orton","Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK",R1_two_fas,,MJT,competed DCE,T1,VFA,nonlinear,OG_MO_AUMC_ICR_RMH,"Oliver Gurney-Champion, Matthew Orton","Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK",R1_VFA,,MJT,competed -DCE,T1,VFA,linear,ST_SydneyAus_T1,Sirisha Tadimalla,"University of Sydney, Australia",VFAT1mapping,,MJT,completed -DCE,T1,VFA,nonlinear,ST_SydneyAus_T1,Sirisha Tadimalla,"University of Sydney, Australia",VFAT1mapping,,MJT,completed +DCE,T1,VFA,linear,ST_Sydney_AUS_T1,Sirisha Tadimalla,"University of Sydney, Australia",VFAT1mapping,,MJT,completed +DCE,T1,VFA,nonlinear,ST_Sydney_AUS_T1,Sirisha Tadimalla,"University of Sydney, Australia",VFAT1mapping,,MJT,completed DCE/DSC,AIF deconvolution,,,SR_TBG_BNI_PhoenixUSA,"Sudarshan Ragunathan, Laura Bell","Barrow Neurological Institute, USA",AIFdeconvolution,,JA,completed DCE/DSC,Miscellaneous,calculate SNR,,DS_BW_VanderBiltUMC_USA,"David Smith, Brian Welch","VanderBilt University Medical Center, USA",signal_to_noise_ratio,,tbd, DCE/DSC,Miscellaneous,calculate enhancement ratio,,DS_BW_VanderBiltUMC_USA,"David Smith, Brian Welch","VanderBilt University Medical Center, USA",signal_enhancement_ratio,,tbd, diff --git a/notebooks/contributors.ipynb b/notebooks/contributors.ipynb index b793223b..c6f77a34 100644 --- a/notebooks/contributors.ipynb +++ b/notebooks/contributors.ipynb @@ -102,7 +102,7 @@ " Concentration to enhancement\n", " NaN\n", " NaN\n", - " MJT_UoEdinburghUK\n", + " MJT_UoEdinburgh_UK\n", " Michael Thrippleton\n", " University of Edinburgh, UK\n", " tbd\n", @@ -141,7 +141,7 @@ " Concentration to signal\n", " SPGR\n", " NaN\n", - " MB_QBI_UoManchesterUK\n", + " MB_QBI_UoManchester_UK\n", " Michael Berks\n", " University of Manchester, UK\n", " tbd\n", @@ -206,7 +206,7 @@ " Input Functions\n", " load AIF\n", " load from txt\n", - " MB_QBI_UoManchesterUK\n", + " MB_QBI_UoManchester_UK\n", " Michael Berks\n", " University of Manchester, UK\n", " tbd\n", @@ -271,7 +271,7 @@ " Input Functions\n", " Parker AIF\n", " Parker AIF, Parker-like AIF\n", - " MJT_UoEdinburghUK\n", + " MJT_UoEdinburgh_UK\n", " Michael Thrippleton\n", " University of Edinburgh, UK\n", " JK/PvH\n", @@ -284,7 +284,7 @@ " Input Functions\n", " Parker AIF\n", " NaN\n", - " MB_QBI_UoManchesterUK\n", + " MB_QBI_UoManchester_UK\n", " Michael Berks\n", " University of Manchester, UK\n", " JK/PvH\n", @@ -297,7 +297,7 @@ " Input Functions\n", " patient-specific AIF\n", " measured AIF\n", - " MJT_UoEdinburghUK\n", + " MJT_UoEdinburgh_UK\n", " Michael Thrippleton\n", " University of Edinburgh, UK\n", " tbd\n", @@ -323,7 +323,7 @@ " Parameter derivation\n", " iAUC\n", " NaN\n", - " MB_QBI_UoManchesterUK\n", + " MB_QBI_UoManchester_UK\n", " Michael Berks\n", " University of Manchester, UK\n", " tbd\n", @@ -375,7 +375,7 @@ " Pharmacokinetic models\n", " 2-cmp exchange\n", " forward model, NLLS fitting (concentration), N...\n", - " MJT_UoEdinburghUK\n", + " MJT_UoEdinburgh_UK\n", " Michael Thrippleton\n", " University of Edinburgh, UK\n", " tbd\n", @@ -388,7 +388,7 @@ " Pharmacokinetic models\n", " 2-cmp exchange\n", " forward model, LLSQ fitting methods\n", - " MB_QBI_UoManchesterUK\n", + " MB_QBI_UoManchester_UK\n", " Michael Berks\n", " University of Manchester, UK\n", " ST/OGC\n", @@ -401,7 +401,7 @@ " Pharmacokinetic models\n", " 2-cmp filtration\n", " forward model, LLSQ fitting methods\n", - " MB_QBI_UoManchesterUK\n", + " MB_QBI_UoManchester_UK\n", " Michael Berks\n", " University of Manchester, UK\n", " ST/OGC\n", @@ -427,7 +427,7 @@ " Pharmacokinetic models\n", " 2-cmp uptake\n", " forward model, NLLS fitting (concentration), N...\n", - " MJT_UoEdinburghUK\n", + " MJT_UoEdinburgh_UK\n", " Michael Thrippleton\n", " University of Edinburgh, UK\n", " tbd\n", @@ -453,7 +453,7 @@ " Pharmacokinetic models\n", " active uptake and efflux (AUEM)\n", " forward model, LLSQ fitting methods\n", - " MB_QBI_UoManchesterUK\n", + " MB_QBI_UoManchester_UK\n", " Michael Berks\n", " University of Manchester, UK\n", " ST/OGC\n", @@ -492,7 +492,7 @@ " Pharmacokinetic models\n", " dual-inlet general model\n", " works with 2CXM, 2CFM, AUEM, LLSQ fitting methods\n", - " MB_QBI_UoManchesterUK\n", + " MB_QBI_UoManchester_UK\n", " Michael Berks\n", " University of Manchester, UK\n", " ST/OGC\n", @@ -570,7 +570,7 @@ " Pharmacokinetic models\n", " extended Tofts\n", " forward model, NLLS fitting (concentration), N...\n", - " MJT_UoEdinburghUK\n", + " MJT_UoEdinburgh_UK\n", " Michael Thrippleton\n", " University of Edinburgh, UK\n", " ST/OGC\n", @@ -583,7 +583,7 @@ " Pharmacokinetic models\n", " extended Tofts\n", " forward model, LLSQ fitting methods\n", - " MB_QBI_UoManchesterUK\n", + " MB_QBI_UoManchester_UK\n", " Michael Berks\n", " University of Manchester, UK\n", " ST/OGC\n", @@ -635,7 +635,7 @@ " Pharmacokinetic models\n", " Patlak\n", " forward model, NLLS fitting (concentration), N...\n", - " MJT_UoEdinburghUK\n", + " MJT_UoEdinburgh_UK\n", " Michael Thrippleton\n", " University of Edinburgh, UK\n", " tbd\n", @@ -648,7 +648,7 @@ " Pharmacokinetic models\n", " steady-state vp\n", " forward model, NLLS fitting (concentration), N...\n", - " MJT_UoEdinburghUK\n", + " MJT_UoEdinburgh_UK\n", " Michael Thrippleton\n", " University of Edinburgh, UK\n", " tbd\n", @@ -687,7 +687,7 @@ " Pharmacokinetic models\n", " Tofts\n", " forward model, NLLS fitting (concentration), N...\n", - " MJT_UoEdinburghUK\n", + " MJT_UoEdinburgh_UK\n", " Michael Thrippleton\n", " University of Edinburgh, UK\n", " ST/OGC\n", @@ -791,7 +791,7 @@ " Signal to concentration\n", " SPGR\n", " NaN\n", - " MJT_UoEdinburghUK\n", + " MJT_UoEdinburgh_UK\n", " Michael Thrippleton\n", " University of Edinburgh, UK\n", " LK\n", @@ -804,7 +804,7 @@ " Signal to concentration\n", " SPGR\n", " NaN\n", - " MB_QBI_UoManchesterUK\n", + " MB_QBI_UoManchester_UK\n", " Michael Berks\n", " University of Manchester, UK\n", " LK\n", @@ -830,7 +830,7 @@ " Signal to enhancement\n", " NaN\n", " NaN\n", - " MJT_UoEdinburghUK\n", + " MJT_UoEdinburgh_UK\n", " Michael Thrippleton\n", " University of Edinburgh, UK\n", " tbd\n", @@ -882,7 +882,7 @@ " T1\n", " DESPOT1-HIFI\n", " Fit any combination of (IR-)SPGR scans to esti...\n", - " MJT_UoEdinburghUK\n", + " MJT_UoEdinburgh_UK\n", " Michael Thrippleton\n", " University of Edinburgh, UK\n", " MJT\n", @@ -895,7 +895,7 @@ " T1\n", " VFA\n", " linear, nonlinear\n", - " ST_SydneyAus_T1\n", + " ST_Sydney_AUS_T1\n", " Sirisha Tadimalla\n", " University of Sydney, Australia\n", " MJT\n", @@ -908,7 +908,7 @@ " T1\n", " VFA\n", " linear, nonlinear, two flip angles\n", - " MJT_UoEdinburghUK\n", + " MJT_UoEdinburgh_UK\n", " Michael Thrippleton\n", " University of Edinburgh, UK\n", " MJT\n", @@ -1207,52 +1207,52 @@ " Notes Subfolder \\\n", "0 Cheong et al (DOI: 10.1088/0031-9155/48/5/403) LEK_UoEdinburgh \n", "1 NaN LEK_UoEdinburgh \n", - "2 NaN MJT_UoEdinburghUK \n", + "2 NaN MJT_UoEdinburgh_UK \n", "3 NaN OG_MO_AUMC_ICR_RMH \n", "4 NaN LEK_UoEdinburgh \n", - "5 NaN MB_QBI_UoManchesterUK \n", + "5 NaN MB_QBI_UoManchester_UK \n", "6 NaN OG_MO_AUMC_ICR_RMH \n", "7 NaN OG_MO_AUMC_ICR_RMH \n", "8 Georgiou et al (DOI: 10.1002/mrm.27524) PvH_NKI \n", "9 Wong et al (DOI: https://doi.org/10.2967/jnume... OG_MO_AUMC_ICR_RMH \n", - "10 load from txt MB_QBI_UoManchesterUK \n", + "10 load from txt MB_QBI_UoManchester_UK \n", "11 from txt, gamma-variate function OGJ_OsloU_Norway \n", "12 NaN ST_USydAUS_DCE \n", "13 NaN OG_MO_AUMC_ICR_RMH \n", "14 NaN PvH_NKI \n", - "15 Parker AIF, Parker-like AIF MJT_UoEdinburghUK \n", - "16 NaN MB_QBI_UoManchesterUK \n", - "17 measured AIF MJT_UoEdinburghUK \n", + "15 Parker AIF, Parker-like AIF MJT_UoEdinburgh_UK \n", + "16 NaN MB_QBI_UoManchester_UK \n", + "17 measured AIF MJT_UoEdinburgh_UK \n", "18 McGrath et al (DOI: 10.1002/mrm.21959) ST_USydAUS_DCE \n", - "19 NaN MB_QBI_UoManchesterUK \n", + "19 NaN MB_QBI_UoManchester_UK \n", "20 forward model ST_USydAUS_DCE \n", "21 forward model LEK_UoEdinburgh \n", "22 forward model, NLLS and LLSQ fitting methods OGJ_OsloU_Norway \n", - "23 forward model, NLLS fitting (concentration), N... MJT_UoEdinburghUK \n", - "24 forward model, LLSQ fitting methods MB_QBI_UoManchesterUK \n", - "25 forward model, LLSQ fitting methods MB_QBI_UoManchesterUK \n", + "23 forward model, NLLS fitting (concentration), N... MJT_UoEdinburgh_UK \n", + "24 forward model, LLSQ fitting methods MB_QBI_UoManchester_UK \n", + "25 forward model, LLSQ fitting methods MB_QBI_UoManchester_UK \n", "26 forward model LEK_UoEdinburgh \n", - "27 forward model, NLLS fitting (concentration), N... MJT_UoEdinburghUK \n", + "27 forward model, NLLS fitting (concentration), N... MJT_UoEdinburgh_UK \n", "28 forward model LEK_UoEdinburgh \n", - "29 forward model, LLSQ fitting methods MB_QBI_UoManchesterUK \n", + "29 forward model, LLSQ fitting methods MB_QBI_UoManchester_UK \n", "30 forward model ST_USydAUS_DCE \n", "31 forward model ST_USydAUS_DCE \n", - "32 works with 2CXM, 2CFM, AUEM, LLSQ fitting methods MB_QBI_UoManchesterUK \n", + "32 works with 2CXM, 2CFM, AUEM, LLSQ fitting methods MB_QBI_UoManchester_UK \n", "33 forward model ST_USydAUS_DCE \n", "34 forward model LEK_UoEdinburgh \n", "35 forward model ST_USydAUS_DCE \n", "36 forward model, NLLS fitting methods OG_MO_AUMC_ICR_RMH \n", "37 forward model, NLLS and LLSQ fitting methods OGJ_OsloU_Norway \n", - "38 forward model, NLLS fitting (concentration), N... MJT_UoEdinburghUK \n", - "39 forward model, LLSQ fitting methods MB_QBI_UoManchesterUK \n", + "38 forward model, NLLS fitting (concentration), N... MJT_UoEdinburgh_UK \n", + "39 forward model, LLSQ fitting methods MB_QBI_UoManchester_UK \n", "40 forward model ST_USydAUS_DCE \n", "41 forward model LEK_UoEdinburgh \n", "42 forward model ST_USydAUS_DCE \n", - "43 forward model, NLLS fitting (concentration), N... MJT_UoEdinburghUK \n", - "44 forward model, NLLS fitting (concentration), N... MJT_UoEdinburghUK \n", + "43 forward model, NLLS fitting (concentration), N... MJT_UoEdinburgh_UK \n", + "44 forward model, NLLS fitting (concentration), N... MJT_UoEdinburgh_UK \n", "45 forward model LEK_UoEdinburgh \n", "46 forward model, NLLS and LLSQ fitting methods OGJ_OsloU_Norway \n", - "47 forward model, NLLS fitting (concentration), N... MJT_UoEdinburghUK \n", + "47 forward model, NLLS fitting (concentration), N... MJT_UoEdinburgh_UK \n", "48 forward model, NLLS fitting methods LCB_BNI_USA \n", "49 check for enhancement OG_MO_AUMC_ICR_RMH \n", "50 NaN OG_MO_AUMC_ICR_RMH \n", @@ -1260,16 +1260,16 @@ "52 NaN OG_MO_AUMC_ICR_RMH \n", "53 NaN LEK_UoEdinburgh \n", "54 NaN ST_USydAUS_DCE \n", - "55 NaN MJT_UoEdinburghUK \n", - "56 NaN MB_QBI_UoManchesterUK \n", + "55 NaN MJT_UoEdinburgh_UK \n", + "56 NaN MB_QBI_UoManchester_UK \n", "57 NaN LCB_BNI_USA \n", - "58 NaN MJT_UoEdinburghUK \n", + "58 NaN MJT_UoEdinburgh_UK \n", "59 NaN ST_USydAUS_DCE \n", "60 NaN OG_MO_AUMC_ICR_RMH \n", "61 NaN LCB_BNI_USA \n", - "62 Fit any combination of (IR-)SPGR scans to esti... MJT_UoEdinburghUK \n", - "63 linear, nonlinear ST_SydneyAus_T1 \n", - "64 linear, nonlinear, two flip angles MJT_UoEdinburghUK \n", + "62 Fit any combination of (IR-)SPGR scans to esti... MJT_UoEdinburgh_UK \n", + "63 linear, nonlinear ST_Sydney_AUS_T1 \n", + "64 linear, nonlinear, two flip angles MJT_UoEdinburgh_UK \n", "65 two flip angles OG_MO_AUMC_ICR_RMH \n", "66 despot, novifast McGill_VFA \n", "67 NaN SR_TBG_BNI_PhoenixUSA \n", diff --git a/src/original/JBJA_GUSahlgrenskaSWE/AIF_selection_auto/AIF_selection_automatic.py b/src/original/JBJA_GUSahlgrenska_SWE/AIF_selection_auto/AIF_selection_automatic.py similarity index 100% rename from src/original/JBJA_GUSahlgrenskaSWE/AIF_selection_auto/AIF_selection_automatic.py rename to src/original/JBJA_GUSahlgrenska_SWE/AIF_selection_auto/AIF_selection_automatic.py diff --git a/src/original/JBJA_GUSahlgrenskaSWE/AIF_selection_auto/__init__.py b/src/original/JBJA_GUSahlgrenska_SWE/AIF_selection_auto/__init__.py similarity index 100% rename from src/original/JBJA_GUSahlgrenskaSWE/AIF_selection_auto/__init__.py rename to src/original/JBJA_GUSahlgrenska_SWE/AIF_selection_auto/__init__.py diff --git 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diff --git a/src/original/JBJA_GUSahlgrenskaSWE/AIF_selection_auto/demo/demo.ipynb b/src/original/JBJA_GUSahlgrenska_SWE/AIF_selection_auto/demo/demo.ipynb similarity index 100% rename from src/original/JBJA_GUSahlgrenskaSWE/AIF_selection_auto/demo/demo.ipynb rename to src/original/JBJA_GUSahlgrenska_SWE/AIF_selection_auto/demo/demo.ipynb diff --git a/src/original/JBJA_GUSahlgrenskaSWE/AIF_selection_auto/demo/plots.py b/src/original/JBJA_GUSahlgrenska_SWE/AIF_selection_auto/demo/plots.py similarity index 100% rename from src/original/JBJA_GUSahlgrenskaSWE/AIF_selection_auto/demo/plots.py rename to src/original/JBJA_GUSahlgrenska_SWE/AIF_selection_auto/demo/plots.py diff --git a/src/original/JBJA_GUSahlgrenskaSWE/AIF_selection_auto/plots.py b/src/original/JBJA_GUSahlgrenska_SWE/AIF_selection_auto/plots.py similarity index 100% rename from src/original/JBJA_GUSahlgrenskaSWE/AIF_selection_auto/plots.py rename to src/original/JBJA_GUSahlgrenska_SWE/AIF_selection_auto/plots.py diff --git a/src/original/LEK_UoEdinburghUK/PharmacokineticModelling/BAT_estimation.py b/src/original/LEK_UoEdinburgh_UK/PharmacokineticModelling/BAT_estimation.py similarity index 100% rename from src/original/LEK_UoEdinburghUK/PharmacokineticModelling/BAT_estimation.py rename to src/original/LEK_UoEdinburgh_UK/PharmacokineticModelling/BAT_estimation.py diff --git a/src/original/LEK_UoEdinburghUK/PharmacokineticModelling/__init__.py b/src/original/LEK_UoEdinburgh_UK/PharmacokineticModelling/__init__.py similarity index 100% rename from src/original/LEK_UoEdinburghUK/PharmacokineticModelling/__init__.py rename to src/original/LEK_UoEdinburgh_UK/PharmacokineticModelling/__init__.py diff --git a/src/original/LEK_UoEdinburghUK/PharmacokineticModelling/models.py b/src/original/LEK_UoEdinburgh_UK/PharmacokineticModelling/models.py similarity index 100% rename from src/original/LEK_UoEdinburghUK/PharmacokineticModelling/models.py rename to 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diff --git a/src/original/MJT_UoEdinburghUK/pk_models.py b/src/original/MJT_UoEdinburgh_UK/pk_models.py similarity index 100% rename from src/original/MJT_UoEdinburghUK/pk_models.py rename to src/original/MJT_UoEdinburgh_UK/pk_models.py diff --git a/src/original/MJT_UoEdinburghUK/relaxivity.py b/src/original/MJT_UoEdinburgh_UK/relaxivity.py similarity index 100% rename from src/original/MJT_UoEdinburghUK/relaxivity.py rename to src/original/MJT_UoEdinburgh_UK/relaxivity.py diff --git a/src/original/MJT_UoEdinburghUK/signal_models.py b/src/original/MJT_UoEdinburgh_UK/signal_models.py similarity index 100% rename from src/original/MJT_UoEdinburghUK/signal_models.py rename to src/original/MJT_UoEdinburgh_UK/signal_models.py diff --git a/src/original/MJT_UoEdinburghUK/t1_fit.py b/src/original/MJT_UoEdinburgh_UK/t1_fit.py similarity index 100% rename from src/original/MJT_UoEdinburghUK/t1_fit.py rename to src/original/MJT_UoEdinburgh_UK/t1_fit.py diff --git 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src/original/SR_TBG_BNIPhoenix_USA/DSCparameters/DSC_parameters.py diff --git a/src/original/SR_TBG_BNIPhoenixUSA/DSCparameters/__init__.py b/src/original/SR_TBG_BNIPhoenix_USA/DSCparameters/__init__.py similarity index 100% rename from src/original/SR_TBG_BNIPhoenixUSA/DSCparameters/__init__.py rename to src/original/SR_TBG_BNIPhoenix_USA/DSCparameters/__init__.py diff --git a/src/original/SR_TBG_BNIPhoenixUSA/LeakageCorrection/__init__.py b/src/original/SR_TBG_BNIPhoenix_USA/LeakageCorrection/__init__.py similarity index 100% rename from src/original/SR_TBG_BNIPhoenixUSA/LeakageCorrection/__init__.py rename to src/original/SR_TBG_BNIPhoenix_USA/LeakageCorrection/__init__.py diff --git a/src/original/SR_TBG_BNIPhoenixUSA/LeakageCorrection/bsw_leakagecorr.py b/src/original/SR_TBG_BNIPhoenix_USA/LeakageCorrection/bsw_leakagecorr.py similarity index 100% rename from src/original/SR_TBG_BNIPhoenixUSA/LeakageCorrection/bsw_leakagecorr.py rename to src/original/SR_TBG_BNIPhoenix_USA/LeakageCorrection/bsw_leakagecorr.py diff --git a/src/original/SR_TBG_BNIPhoenixUSA/LeakageCorrection/requirements.txt b/src/original/SR_TBG_BNIPhoenix_USA/LeakageCorrection/requirements.txt similarity index 100% rename from src/original/SR_TBG_BNIPhoenixUSA/LeakageCorrection/requirements.txt rename to src/original/SR_TBG_BNIPhoenix_USA/LeakageCorrection/requirements.txt diff --git a/src/original/SR_TBG_BNIPhoenixUSA/__init__.py b/src/original/SR_TBG_BNIPhoenix_USA/__init__.py similarity index 100% rename from src/original/SR_TBG_BNIPhoenixUSA/__init__.py rename to src/original/SR_TBG_BNIPhoenix_USA/__init__.py diff --git a/src/original/ST_USydAUS/InputFunctions.py b/src/original/ST_USyd_AUS/InputFunctions.py similarity index 100% rename from src/original/ST_USydAUS/InputFunctions.py rename to src/original/ST_USyd_AUS/InputFunctions.py diff --git a/src/original/ST_USydAUS/ModelDictionary.py b/src/original/ST_USyd_AUS/ModelDictionary.py similarity index 100% rename from src/original/ST_USydAUS/ModelDictionary.py rename to src/original/ST_USyd_AUS/ModelDictionary.py diff --git a/src/original/ST_USydAUS/Tools.py b/src/original/ST_USyd_AUS/Tools.py similarity index 100% rename from src/original/ST_USydAUS/Tools.py rename to src/original/ST_USyd_AUS/Tools.py diff --git a/src/original/ST_USydAUS/VFAT1mapping.py b/src/original/ST_USyd_AUS/VFAT1mapping.py similarity index 100% rename from src/original/ST_USydAUS/VFAT1mapping.py rename to src/original/ST_USyd_AUS/VFAT1mapping.py diff --git a/src/original/ST_USydAUS/__init__.py b/src/original/ST_USyd_AUS/__init__.py similarity index 100% rename from src/original/ST_USydAUS/__init__.py rename to src/original/ST_USyd_AUS/__init__.py diff --git a/src/original/ST_USydAUS/signals2conc.py b/src/original/ST_USyd_AUS/signals2conc.py similarity index 100% rename from src/original/ST_USydAUS/signals2conc.py rename to src/original/ST_USyd_AUS/signals2conc.py diff --git a/src/wrappers/tofts.py b/src/wrappers/tofts.py index be3cc6b5..ad87305e 100644 --- a/src/wrappers/tofts.py +++ b/src/wrappers/tofts.py @@ -6,14 +6,14 @@ # osipi utilities from osipi_code_collection.utils.nb import percenterror # osipi implementations -import osipi_code_collection.original.LEK_UoEdinburghUK.PharmacokineticModelling.models as edinburgh1 -import osipi_code_collection.original.MJT_UoEdinburghUK.aifs as edinburgh2_aifs -import osipi_code_collection.original.MJT_UoEdinburghUK.pk_models as edinburgh2_models -import osipi_code_collection.original.MJT_UoEdinburghUK.dce_fit as edinburgh2_fit +import osipi_code_collection.original.LEK_UoEdinburgh_UK.PharmacokineticModelling.models as edinburgh1 +import osipi_code_collection.original.MJT_UoEdinburgh_UK.aifs as edinburgh2_aifs +import osipi_code_collection.original.MJT_UoEdinburgh_UK.pk_models as edinburgh2_models +import osipi_code_collection.original.MJT_UoEdinburgh_UK.dce_fit as edinburgh2_fit import osipi_code_collection.original.OGJ_OsloU_NOR.MRImageAnalysis.DCE.Analyze as oslo import osipi_code_collection.original.ST_USydAUS.ModelDictionary as sydney -from osipi_code_collection.original.MB_QBI_UoManchesterUK.QbiPy.dce_models import dce_aif as manchester_aif -from osipi_code_collection.original.MB_QBI_UoManchesterUK.QbiPy.dce_models import tofts_model as manchester_tofts +from osipi_code_collection.original.MB_QBI_UoManchester_UK.QbiPy.dce_models import dce_aif as manchester_aif +from osipi_code_collection.original.MB_QBI_UoManchester_UK.QbiPy.dce_models import tofts_model as manchester_tofts import osipi_code_collection.original.OG_MO_AUMC_ICR_RMH_NL_UK.ExtendedTofts.DCE as amsterdam def tofts_fit(author, ct = None, ca = None, t = None, fittype = "linear", mask = None, data = None): diff --git a/src/wrappers/vfa.py b/src/wrappers/vfa.py index e72c09c2..d4b3fbe4 100644 --- a/src/wrappers/vfa.py +++ b/src/wrappers/vfa.py @@ -1,4 +1,4 @@ -import osipi_code_collection.original.MJT_UoEdinburghUK.t1_fit as edinburgh +import osipi_code_collection.original.MJT_UoEdinburgh_UK.t1_fit as edinburgh import osipi_code_collection.original.ST_USydAUS.VFAT1mapping as sydney import osipi_code_collection.original.McGill_CAN.vfa as mcgill from osipi_code_collection.utils.nb import percenterror diff --git a/test/DCEmodels/test_DCEmodels_2CUM_LEK_UoEdinburghUK.py b/test/DCEmodels/test_DCEmodels_2CUM_LEK_UoEdinburgh_UK.py similarity index 92% rename from test/DCEmodels/test_DCEmodels_2CUM_LEK_UoEdinburghUK.py rename to test/DCEmodels/test_DCEmodels_2CUM_LEK_UoEdinburgh_UK.py index f09d4699..c3d353ca 100644 --- a/test/DCEmodels/test_DCEmodels_2CUM_LEK_UoEdinburghUK.py +++ b/test/DCEmodels/test_DCEmodels_2CUM_LEK_UoEdinburgh_UK.py @@ -5,7 +5,7 @@ from time import perf_counter from ..helpers import osipi_parametrize, log_init, log_results from . import DCEmodels_data -from src.original.LEK_UoEdinburghUK.PharmacokineticModelling.models import TwoCUM +from src.original.LEK_UoEdinburgh_UK.PharmacokineticModelling.models import TwoCUM arg_names = 'label, t_array, C_t_array, cp_aif_array, vp_ref, fp_ref, ' \ 'delay_ref, ps_ref, a_tol_vp, r_tol_vp, a_tol_fp, r_tol_fp,'\ @@ -18,13 +18,13 @@ def setup_module(module): global filename_prefix # we want to change the global variable os.makedirs('./test/results/DCEmodels', exist_ok=True) filename_prefix = 'DCEmodels/TestResults_models' - log_init(filename_prefix, '_LEK_UoEdinburghUK_2CUM', ['label', 'time (us)', 'vp_ref', 'fp_ref', 'ps_ref', 'delay_ref', 'vp_meas', 'fp_meas', 'ps_meas', 'delay_meas']) + log_init(filename_prefix, '_LEK_UoEdinburgh_UK_2CUM', ['label', 'time (us)', 'vp_ref', 'fp_ref', 'ps_ref', 'delay_ref', 'vp_meas', 'fp_meas', 'ps_meas', 'delay_meas']) test_data = (DCEmodels_data.dce_DRO_data_2cum()) # Use the test data to generate a parametrize decorator. This causes the following # test to be run for every test case listed in test_data... @osipi_parametrize(arg_names, test_data, xf_labels=[]) -def test_LEK_UoEdinburghUK_2cum_model(label, t_array, C_t_array, +def test_LEK_UoEdinburgh_UK_2cum_model(label, t_array, C_t_array, cp_aif_array, vp_ref, fp_ref, ps_ref, delay_ref, a_tol_vp, r_tol_vp, a_tol_fp, r_tol_fp, a_tol_ps, r_tol_ps, @@ -63,7 +63,7 @@ def test_LEK_UoEdinburghUK_2cum_model(label, t_array, C_t_array, exc_time = 1e6 * (perf_counter() - tic) # measure execution time # log results - log_results(filename_prefix, '_LEK_UoEdinburghUK_2CUM', [ + log_results(filename_prefix, '_LEK_UoEdinburgh_UK_2CUM', [ [label, f"{exc_time:.0f}", vp_ref, fp_ref, ps_ref, delay_ref, vp_meas, fp_meas, ps_meas, delay_ref]]) # run test @@ -79,7 +79,7 @@ def test_LEK_UoEdinburghUK_2cum_model(label, t_array, C_t_array, # Use the test data to generate a parametrize decorator. This causes the following # test to be run for every test case listed in test_data... @osipi_parametrize(arg_names, test_data_delay, xf_labels=[]) -def test_LEK_UoEdinburghUK_2cum_model_delay(label, t_array, C_t_array, +def test_LEK_UoEdinburgh_UK_2cum_model_delay(label, t_array, C_t_array, cp_aif_array, vp_ref, fp_ref, ps_ref, delay_ref, a_tol_vp, r_tol_vp, a_tol_fp, r_tol_fp, a_tol_ps, r_tol_ps, @@ -119,7 +119,7 @@ def test_LEK_UoEdinburghUK_2cum_model_delay(label, t_array, C_t_array, exc_time = 1e6 * (perf_counter() - tic) # measure execution time # log results - log_results(filename_prefix, '_LEK_UoEdinburghUK_2CUM', [ + log_results(filename_prefix, '_LEK_UoEdinburgh_UK_2CUM', [ [label, f"{exc_time:.0f}", vp_ref, fp_ref, ps_ref, delay_ref, vp_meas, fp_meas, ps_meas, delay_meas]]) # run test diff --git a/test/DCEmodels/test_DCEmodels_2CUM_MJT_UoEdinburghUK.py b/test/DCEmodels/test_DCEmodels_2CUM_MJT_UoEdinburgh_UK.py similarity index 87% rename from test/DCEmodels/test_DCEmodels_2CUM_MJT_UoEdinburghUK.py rename to test/DCEmodels/test_DCEmodels_2CUM_MJT_UoEdinburgh_UK.py index a87c53ee..e0494d08 100644 --- a/test/DCEmodels/test_DCEmodels_2CUM_MJT_UoEdinburghUK.py +++ b/test/DCEmodels/test_DCEmodels_2CUM_MJT_UoEdinburgh_UK.py @@ -3,7 +3,7 @@ from time import perf_counter from ..helpers import osipi_parametrize, log_init, log_results from . import DCEmodels_data -from src.original.MJT_UoEdinburghUK import dce_fit, pk_models, aifs +from src.original.MJT_UoEdinburgh_UK import dce_fit, pk_models, aifs arg_names = 'label, t_array, C_t_array, cp_aif_array, vp_ref, fp_ref, ' \ 'delay_ref, ps_ref, a_tol_vp, r_tol_vp, a_tol_fp, r_tol_fp,'\ @@ -17,14 +17,14 @@ def setup_module(module): global filename_prefix # we want to change the global variable os.makedirs('./test/results/DCEmodels', exist_ok=True) filename_prefix = 'DCEmodels/TestResults_models' - log_init(filename_prefix, '_MJT_UoEdinburghUK_2CUM', ['label', 'time (us)', 'vp_ref', 'fp_ref', 'ps_ref', 'delay_ref', 'vp_meas', 'fp_meas', 'ps_meas', 'delay_meas']) + log_init(filename_prefix, '_MJT_UoEdinburgh_UK_2CUM', ['label', 'time (us)', 'vp_ref', 'fp_ref', 'ps_ref', 'delay_ref', 'vp_meas', 'fp_meas', 'ps_meas', 'delay_meas']) test_data = (DCEmodels_data.dce_DRO_data_2cum()) # Use the test data to generate a parametrize decorator. This causes the following # test to be run for every test case listed in test_data... @osipi_parametrize(arg_names, test_data, xf_labels=[]) -def test_MJT_UoEdinburghUK_2cum_model(label, t_array, C_t_array, +def test_MJT_UoEdinburgh_UK_2cum_model(label, t_array, C_t_array, cp_aif_array, vp_ref, fp_ref, ps_ref, delay_ref, a_tol_vp, r_tol_vp, a_tol_fp, r_tol_fp, a_tol_ps, r_tol_ps, @@ -41,7 +41,7 @@ def test_MJT_UoEdinburghUK_2cum_model(label, t_array, C_t_array, exc_time = 1e6 * (perf_counter() - tic) # measure execution time # log results - log_results(filename_prefix, '_MJT_UoEdinburghUK_2CUM', [ + log_results(filename_prefix, '_MJT_UoEdinburgh_UK_2CUM', [ [label, f"{exc_time:.0f}", vp_ref, fp_ref, ps_ref, delay_ref, vp_meas, fp_meas, ps_meas, delay_ref]]) # run test @@ -57,7 +57,7 @@ def test_MJT_UoEdinburghUK_2cum_model(label, t_array, C_t_array, # Use the test data to generate a parametrize decorator. This causes the following # test to be run for every test case listed in test_data... @osipi_parametrize(arg_names, test_data_delay, xf_labels=[]) -def test_MJT_UoEdinburghUK_2cum_mode_delay(label, t_array, C_t_array, +def test_MJT_UoEdinburgh_UK_2cum_mode_delay(label, t_array, C_t_array, cp_aif_array, vp_ref, fp_ref, ps_ref, delay_ref, a_tol_vp, r_tol_vp, a_tol_fp, r_tol_fp, a_tol_ps, r_tol_ps, @@ -74,7 +74,7 @@ def test_MJT_UoEdinburghUK_2cum_mode_delay(label, t_array, C_t_array, exc_time = 1e6 * (perf_counter() - tic) # measure execution time # log results - log_results(filename_prefix, '_MJT_UoEdinburghUK_2CUM', [ + log_results(filename_prefix, '_MJT_UoEdinburgh_UK_2CUM', [ [label, f"{exc_time:.0f}", vp_ref, fp_ref, ps_ref, delay_ref, vp_meas, fp_meas, ps_meas, delay_ref]]) # run test diff --git a/test/DCEmodels/test_DCEmodels_2CXM_LEK_UoEdinburghUK.py b/test/DCEmodels/test_DCEmodels_2CXM_LEK_UoEdinburgh_UK.py similarity index 92% rename from test/DCEmodels/test_DCEmodels_2CXM_LEK_UoEdinburghUK.py rename to test/DCEmodels/test_DCEmodels_2CXM_LEK_UoEdinburgh_UK.py index dda9928f..28d070b7 100644 --- a/test/DCEmodels/test_DCEmodels_2CXM_LEK_UoEdinburghUK.py +++ b/test/DCEmodels/test_DCEmodels_2CXM_LEK_UoEdinburgh_UK.py @@ -5,7 +5,7 @@ from time import perf_counter from ..helpers import osipi_parametrize, log_init, log_results from . import DCEmodels_data -from src.original.LEK_UoEdinburghUK.PharmacokineticModelling.models import \ +from src.original.LEK_UoEdinburgh_UK.PharmacokineticModelling.models import \ TwoCXM arg_names = 'label, t_array, C_t_array, cp_aif_array, vp_ref, ve_ref, fp_ref,' \ @@ -20,7 +20,7 @@ def setup_module(module): global filename_prefix # we want to change the global variable os.makedirs('./test/results/DCEmodels', exist_ok=True) filename_prefix = 'DCEmodels/TestResults_models' - log_init(filename_prefix, '_LEK_UoEdinburghUK_2CXM', ['label', 'time (us)', 'vp_ref', 've_ref', 'fp_ref', 'ps_ref','delay_ref', 'vp_meas', 've_meas', 'fp_meas', 'ps_meas','delay_meas']) + log_init(filename_prefix, '_LEK_UoEdinburgh_UK_2CXM', ['label', 'time (us)', 'vp_ref', 've_ref', 'fp_ref', 'ps_ref','delay_ref', 'vp_meas', 've_meas', 'fp_meas', 'ps_meas','delay_meas']) @@ -28,7 +28,7 @@ def setup_module(module): # Use the test data to generate a parametrize decorator. This causes the # following test to be run for every test case listed in test_data... @osipi_parametrize(arg_names, test_data, xf_labels=[]) -def test_LEK_UoEdinburghUK_2cxm_model(label, t_array, C_t_array, +def test_LEK_UoEdinburgh_UK_2cxm_model(label, t_array, C_t_array, cp_aif_array, vp_ref, ve_ref, fp_ref, ps_ref, delay_ref, a_tol_vp, r_tol_vp, a_tol_ve, @@ -68,7 +68,7 @@ def test_LEK_UoEdinburghUK_2cxm_model(label, t_array, C_t_array, exc_time = 1e6 * (perf_counter() - tic) # measure execution time # log results - log_results(filename_prefix, '_LEK_UoEdinburghUK_2CXM', [ + log_results(filename_prefix, '_LEK_UoEdinburgh_UK_2CXM', [ [label, f"{exc_time:.0f}", vp_ref, ve_ref, fp_ref, ps_ref, delay_ref, vp_meas, ve_meas, fp_meas, ps_meas, delay_ref]]) @@ -85,7 +85,7 @@ def test_LEK_UoEdinburghUK_2cxm_model(label, t_array, C_t_array, test_data_delay = (DCEmodels_data.dce_DRO_data_2cxm(delay=True)) @osipi_parametrize(arg_names, test_data_delay, xf_labels=[]) -def test_LEK_UoEdinburghUK_2cxm_model_delay(label, t_array, C_t_array, +def test_LEK_UoEdinburgh_UK_2cxm_model_delay(label, t_array, C_t_array, cp_aif_array, vp_ref, ve_ref, fp_ref, ps_ref, delay_ref, a_tol_vp, r_tol_vp, a_tol_ve, @@ -128,7 +128,7 @@ def test_LEK_UoEdinburghUK_2cxm_model_delay(label, t_array, C_t_array, exc_time = 1e6 * (perf_counter() - tic) # measure execution time # log results - log_results(filename_prefix, '_LEK_UoEdinburghUK_2CXM', [ + log_results(filename_prefix, '_LEK_UoEdinburgh_UK_2CXM', [ [label, f"{exc_time:.0f}", vp_ref, ve_ref, fp_ref, ps_ref, delay_ref, vp_meas, ve_meas, fp_meas, ps_meas, delay_meas]]) # run tests diff --git a/test/DCEmodels/test_DCEmodels_2CXM_MB_QBI_UoManchesterUK.py b/test/DCEmodels/test_DCEmodels_2CXM_MB_QBI_UoManchester_UK.py similarity index 86% rename from test/DCEmodels/test_DCEmodels_2CXM_MB_QBI_UoManchesterUK.py rename to test/DCEmodels/test_DCEmodels_2CXM_MB_QBI_UoManchester_UK.py index 519651bb..7c0df617 100644 --- a/test/DCEmodels/test_DCEmodels_2CXM_MB_QBI_UoManchesterUK.py +++ b/test/DCEmodels/test_DCEmodels_2CXM_MB_QBI_UoManchester_UK.py @@ -3,7 +3,7 @@ from time import perf_counter from ..helpers import osipi_parametrize, log_init, log_results from . import DCEmodels_data -from src.original.MB_QBI_UoManchesterUK.QbiPy.dce_models import two_cxm_model, \ +from src.original.MB_QBI_UoManchester_UK.QbiPy.dce_models import two_cxm_model, \ dce_aif arg_names = 'label, t_array, C_t_array, cp_aif_array, vp_ref, ve_ref, fp_ref,' \ @@ -19,13 +19,13 @@ def setup_module(module): global filename_prefix # we want to change the global variable os.makedirs('./test/results/DCEmodels', exist_ok=True) filename_prefix = 'DCEmodels/TestResults_models' - log_init(filename_prefix, '_MB_QBI_UoManchesterUK_2CXM', ['label', 'time (us)', 'vp_ref', 've_ref', 'fp_ref', 'ps_ref', 'vp_meas', 've_meas', 'fp_meas', 'ps_meas']) + log_init(filename_prefix, '_MB_QBI_UoManchester_UK_2CXM', ['label', 'time (us)', 'vp_ref', 've_ref', 'fp_ref', 'ps_ref', 'vp_meas', 've_meas', 'fp_meas', 'ps_meas']) test_data = (DCEmodels_data.dce_DRO_data_2cxm()) # Use the test data to generate a parametrize decorator. This causes the following # test to be run for every test case listed in test_data... @osipi_parametrize(arg_names, test_data, xf_labels=[]) -def test_MB_QBI_UoManchesterUK_2cxm_model(label, t_array, C_t_array, +def test_MB_QBI_UoManchester_UK_2cxm_model(label, t_array, C_t_array, cp_aif_array, vp_ref, ve_ref, fp_ref, ps_ref, delay_ref, a_tol_vp, r_tol_vp, a_tol_ve, @@ -47,7 +47,7 @@ def test_MB_QBI_UoManchesterUK_2cxm_model(label, t_array, C_t_array, exc_time = 1e6 * (perf_counter() - tic) # measure execution time # log results - log_results(filename_prefix, '_MB_QBI_UoManchesterUK_2CXM', [ + log_results(filename_prefix, '_MB_QBI_UoManchester_UK_2CXM', [ [label, f"{exc_time:.0f}", vp_ref, ve_ref, fp_ref, ps_ref, vp_meas, ve_meas, fp_meas, ps_meas]]) # run test diff --git a/test/DCEmodels/test_DCEmodels_2CXM_MJT_UoEdinburghUK.py b/test/DCEmodels/test_DCEmodels_2CXM_MJT_UoEdinburgh_UK.py similarity index 91% rename from test/DCEmodels/test_DCEmodels_2CXM_MJT_UoEdinburghUK.py rename to test/DCEmodels/test_DCEmodels_2CXM_MJT_UoEdinburgh_UK.py index 0fa76c05..3c9bd3c8 100644 --- a/test/DCEmodels/test_DCEmodels_2CXM_MJT_UoEdinburghUK.py +++ b/test/DCEmodels/test_DCEmodels_2CXM_MJT_UoEdinburgh_UK.py @@ -3,7 +3,7 @@ from time import perf_counter from ..helpers import osipi_parametrize, log_init, log_results from . import DCEmodels_data -from src.original.MJT_UoEdinburghUK import dce_fit, pk_models, aifs +from src.original.MJT_UoEdinburgh_UK import dce_fit, pk_models, aifs arg_names = 'label, t_array, C_t_array, cp_aif_array, vp_ref, ve_ref, fp_ref,' \ 'ps_ref, delay_ref, a_tol_vp, r_tol_vp, a_tol_ve, r_tol_ve, ' \ @@ -18,14 +18,14 @@ def setup_module(module): global filename_prefix # we want to change the global variable os.makedirs('./test/results/DCEmodels', exist_ok=True) filename_prefix = 'DCEmodels/TestResults_models' - log_init(filename_prefix, '_MJT_UoEdinburghUK_2CXM', + log_init(filename_prefix, '_MJT_UoEdinburgh_UK_2CXM', ['label', 'time (us)', 'vp_ref', 've_ref', 'fp_ref', 'ps_ref','delay_ref', 'vp_meas', 've_meas', 'fp_meas', 'ps_meas','delay_meas']) test_data = (DCEmodels_data.dce_DRO_data_2cxm()) # Use the test data to generate a parametrize decorator. This causes the following # test to be run for every test case listed in test_data... @osipi_parametrize(arg_names, test_data, xf_labels=[]) -def test_MJT_UoEdinburghUK_2cxm_model(label, t_array, C_t_array, +def test_MJT_UoEdinburgh_UK_2cxm_model(label, t_array, C_t_array, cp_aif_array, vp_ref, ve_ref, fp_ref, ps_ref, delay_ref, a_tol_vp, r_tol_vp, a_tol_ve, @@ -44,7 +44,7 @@ def test_MJT_UoEdinburghUK_2cxm_model(label, t_array, C_t_array, exc_time = 1e6 * (perf_counter() - tic) # measure execution time # log results - log_results(filename_prefix, '_MJT_UoEdinburghUK_2CXM', [ + log_results(filename_prefix, '_MJT_UoEdinburgh_UK_2CXM', [ [label, f"{exc_time:.0f}", vp_ref, ve_ref, fp_ref, ps_ref, delay_ref, vp_meas, ve_meas, fp_meas, ps_meas, delay_ref]]) # run test @@ -62,7 +62,7 @@ def test_MJT_UoEdinburghUK_2cxm_model(label, t_array, C_t_array, # Use the test data to generate a parametrize decorator. This causes the following # test to be run for every test case listed in test_data... @osipi_parametrize(arg_names, test_data_delay, xf_labels=[]) -def test_MJT_UoEdinburghUK_2cxm_model_delay(label, t_array, C_t_array, +def test_MJT_UoEdinburgh_UK_2cxm_model_delay(label, t_array, C_t_array, cp_aif_array, vp_ref, ve_ref, fp_ref, ps_ref, delay_ref, a_tol_vp, r_tol_vp, a_tol_ve, @@ -81,7 +81,7 @@ def test_MJT_UoEdinburghUK_2cxm_model_delay(label, t_array, C_t_array, exc_time = 1e6 * (perf_counter() - tic) # measure execution time # log results - log_results(filename_prefix, '_MJT_UoEdinburghUK_2CXM', [ + log_results(filename_prefix, '_MJT_UoEdinburgh_UK_2CXM', [ [label, f"{exc_time:.0f}", vp_ref, ve_ref, fp_ref, ps_ref, delay_ref, vp_meas, ve_meas, fp_meas, ps_meas, delay_meas]]) # run test diff --git a/test/DCEmodels/test_DCEmodels_2CXM_OGJ_OsloU_NOR.py b/test/DCEmodels/test_DCEmodels_2CXM_OGJ_OsloU_NOR.py index baa7aa9d..cbcd8929 100644 --- a/test/DCEmodels/test_DCEmodels_2CXM_OGJ_OsloU_NOR.py +++ b/test/DCEmodels/test_DCEmodels_2CXM_OGJ_OsloU_NOR.py @@ -50,7 +50,7 @@ def test_OGJ_OsloU_NOR_2cxm_model_llsq(label, t_array, C_t_array, exc_time = 1e6 * (perf_counter() - tic) # measure execution time # log results - log_results(filename_prefix, '_OGJ_OsloU_Norway_2CXM_LLSQ', [ + log_results(filename_prefix, '_OGJ_OsloU_NOR_2CXM_LLSQ', [ [label, f"{exc_time:.0f}", vp_ref, ve_ref, fp_ref, ps_ref, vp_meas, ve_meas, fp_meas, ps_meas]]) # run test diff --git a/test/DCEmodels/test_DCEmodels_Patlak_LEK_UoEdinburghUK.py b/test/DCEmodels/test_DCEmodels_Patlak_LEK_UoEdinburgh_UK.py similarity index 88% rename from test/DCEmodels/test_DCEmodels_Patlak_LEK_UoEdinburghUK.py rename to test/DCEmodels/test_DCEmodels_Patlak_LEK_UoEdinburgh_UK.py index aa78d4f1..bdbacff4 100644 --- a/test/DCEmodels/test_DCEmodels_Patlak_LEK_UoEdinburghUK.py +++ b/test/DCEmodels/test_DCEmodels_Patlak_LEK_UoEdinburgh_UK.py @@ -4,7 +4,7 @@ from time import perf_counter from ..helpers import osipi_parametrize, log_init, log_results from . import DCEmodels_data -from src.original.LEK_UoEdinburghUK.PharmacokineticModelling.models import \ +from src.original.LEK_UoEdinburgh_UK.PharmacokineticModelling.models import \ Patlak arg_names = 'label, t_array, C_t_array, cp_aif_array, vp_ref, ps_ref, ' \ @@ -20,14 +20,14 @@ def setup_module(module): global filename_prefix # we want to change the global variable os.makedirs('./test/results/DCEmodels', exist_ok=True) filename_prefix = 'DCEmodels/TestResults_models' - log_init(filename_prefix, '_LEK_UoEdinburghUK_patlak', ['label', 'time (us)', 'vp_ref', 'ps_ref', 'delay_ref', 'vp_meas', 'ps_meas', 'delay_meas']) + log_init(filename_prefix, '_LEK_UoEdinburgh_UK_patlak', ['label', 'time (us)', 'vp_ref', 'ps_ref', 'delay_ref', 'vp_meas', 'ps_meas', 'delay_meas']) # Use the test data to generate a parametrize decorator. This causes the following # test to be run for every test case listed in test_data... test_data = (DCEmodels_data.dce_DRO_data_Patlak()) @osipi_parametrize(arg_names, test_data, xf_labels=[]) -def test_LEK_UoEdinburghUK_Patlak_model(label, t_array, C_t_array, cp_aif_array, +def test_LEK_UoEdinburgh_UK_Patlak_model(label, t_array, C_t_array, cp_aif_array, vp_ref, ps_ref, delay_ref, a_tol_vp, r_tol_vp, a_tol_ps, r_tol_ps, a_tol_delay, r_tol_delay): @@ -49,7 +49,7 @@ def test_LEK_UoEdinburghUK_Patlak_model(label, t_array, C_t_array, cp_aif_array, exc_time = 1e6 * (perf_counter() - tic) # measure execution time # log results - log_results(filename_prefix, '_LEK_UoEdinburghUK_patlak', [ + log_results(filename_prefix, '_LEK_UoEdinburgh_UK_patlak', [ [label, f"{exc_time:.0f}", vp_ref, ps_ref, delay_ref, vp_meas, ps_meas, delay_ref]]) # in this case delay_ref is used as delay_meas was 0 # run test @@ -63,7 +63,7 @@ def test_LEK_UoEdinburghUK_Patlak_model(label, t_array, C_t_array, cp_aif_array, # Use the test data to generate a parametrize decorator. This causes the # following test to be run for every test case listed in test_data... @osipi_parametrize(arg_names, test_data_delay, xf_labels=[]) -def test_LEK_UoEdinburghUK_Patlak_model_delay(label, t_array, C_t_array, +def test_LEK_UoEdinburgh_UK_Patlak_model_delay(label, t_array, C_t_array, cp_aif_array, vp_ref, ps_ref, delay_ref, a_tol_vp, r_tol_vp, a_tol_ps, r_tol_ps, @@ -88,7 +88,7 @@ def test_LEK_UoEdinburghUK_Patlak_model_delay(label, t_array, C_t_array, exc_time = 1e6 * (perf_counter() - tic) # measure execution time # log results - log_results(filename_prefix, '_LEK_UoEdinburghUK_patlak', [ + log_results(filename_prefix, '_LEK_UoEdinburgh_UK_patlak', [ [label, f"{exc_time:.0f}", vp_ref, ps_ref, delay_ref, vp_meas, ps_meas, delay_meas]]) # run test diff --git a/test/DCEmodels/test_DCEmodels_Patlak_MJT_UoEdinburghUK.py b/test/DCEmodels/test_DCEmodels_Patlak_MJT_UoEdinburgh_UK.py similarity index 84% rename from test/DCEmodels/test_DCEmodels_Patlak_MJT_UoEdinburghUK.py rename to test/DCEmodels/test_DCEmodels_Patlak_MJT_UoEdinburgh_UK.py index bf031607..918a58b3 100644 --- a/test/DCEmodels/test_DCEmodels_Patlak_MJT_UoEdinburghUK.py +++ b/test/DCEmodels/test_DCEmodels_Patlak_MJT_UoEdinburgh_UK.py @@ -3,7 +3,7 @@ from time import perf_counter from ..helpers import osipi_parametrize, log_init, log_results from . import DCEmodels_data -from src.original.MJT_UoEdinburghUK import dce_fit, pk_models, aifs +from src.original.MJT_UoEdinburgh_UK import dce_fit, pk_models, aifs arg_names = 'label, t_array, C_t_array, cp_aif_array, vp_ref, ps_ref, ' \ 'delay_ref, a_tol_vp, r_tol_vp, a_tol_ps, r_tol_ps, a_tol_delay, ' \ @@ -17,13 +17,13 @@ def setup_module(module): global filename_prefix # we want to change the global variable os.makedirs('./test/results/DCEmodels', exist_ok=True) filename_prefix = 'DCEmodels/TestResults_models' - log_init(filename_prefix, '_MJT_UoEdinburghUK_patlak', ['label', 'time (us)', 'vp_ref', 'ps_ref', 'delay_ref', 'vp_meas', 'ps_meas', 'delay_meas']) - log_init(filename_prefix, '_MJT_UoEdinburghUK_patlak_llsq', ['label', 'time (us)', 'vp_ref', 'ps_ref', 'delay_ref', 'vp_meas', 'ps_meas', 'delay_meas']) + log_init(filename_prefix, '_MJT_UoEdinburgh_UK_patlak', ['label', 'time (us)', 'vp_ref', 'ps_ref', 'delay_ref', 'vp_meas', 'ps_meas', 'delay_meas']) + log_init(filename_prefix, '_MJT_UoEdinburgh_UK_patlak_llsq', ['label', 'time (us)', 'vp_ref', 'ps_ref', 'delay_ref', 'vp_meas', 'ps_meas', 'delay_meas']) # Use the test data to generate a parametrize decorator. This causes the following # test to be run for every test case listed in test_data... @osipi_parametrize(arg_names, test_data, xf_labels=[]) -def test_MJT_UoEdinburghUK_Patlak_model(label, t_array, C_t_array, +def test_MJT_UoEdinburgh_UK_Patlak_model(label, t_array, C_t_array, cp_aif_array, vp_ref, ps_ref, delay_ref, a_tol_vp, r_tol_vp, a_tol_ps, r_tol_ps, @@ -40,7 +40,7 @@ def test_MJT_UoEdinburghUK_Patlak_model(label, t_array, C_t_array, exc_time = 1e6 * (perf_counter() - tic) # measure execution time # log results - log_results(filename_prefix, '_MJT_UoEdinburghUK_patlak', [ + log_results(filename_prefix, '_MJT_UoEdinburgh_UK_patlak', [ [label, f"{exc_time:.0f}", vp_ref, ps_ref, delay_ref, vp_meas, ps_meas, delay_ref]]) # run test @@ -54,7 +54,7 @@ def test_MJT_UoEdinburghUK_Patlak_model(label, t_array, C_t_array, # Use the test data to generate a parametrize decorator. This causes the # following test to be run for every test case listed in test_data... @osipi_parametrize(arg_names, test_data_delay, xf_labels=[]) -def test_MJT_UoEdinburghUK_Patlak_model_delay(label, t_array, C_t_array, +def test_MJT_UoEdinburgh_UK_Patlak_model_delay(label, t_array, C_t_array, cp_aif_array, vp_ref, ps_ref, delay_ref, a_tol_vp, r_tol_vp, a_tol_ps, r_tol_ps, @@ -71,7 +71,7 @@ def test_MJT_UoEdinburghUK_Patlak_model_delay(label, t_array, C_t_array, exc_time = 1e6 * (perf_counter() - tic) # measure execution time # log results - log_results(filename_prefix, '_MJT_UoEdinburghUK_patlak', + log_results(filename_prefix, '_MJT_UoEdinburgh_UK_patlak', [[label, f"{exc_time:.0f}", vp_ref, ps_ref, delay_ref, vp_meas, ps_meas, delay_meas]]) # run test @@ -81,7 +81,7 @@ def test_MJT_UoEdinburghUK_Patlak_model_delay(label, t_array, C_t_array, @osipi_parametrize(arg_names, test_data, xf_labels=[]) -def test_MJT_UoEdinburghUK_Patlak_model_llsq(label, t_array, C_t_array, +def test_MJT_UoEdinburgh_UK_Patlak_model_llsq(label, t_array, C_t_array, cp_aif_array, vp_ref, ps_ref, delay_ref, a_tol_vp, r_tol_vp, a_tol_ps, r_tol_ps, @@ -97,7 +97,7 @@ def test_MJT_UoEdinburghUK_Patlak_model_llsq(label, t_array, C_t_array, exc_time = 1e6 * (perf_counter() - tic) # measure execution time # log results - log_results(filename_prefix, '_MJT_UoEdinburghUK_patlak_llsq', [ + log_results(filename_prefix, '_MJT_UoEdinburgh_UK_patlak_llsq', [ [label, f"{exc_time:.0f}", vp_ref, ps_ref, delay_ref, vp_meas, ps_meas, delay_ref]]) # run test diff --git a/test/DCEmodels/test_DCEmodels_Patlak_ST_USydAUS.py b/test/DCEmodels/test_DCEmodels_Patlak_ST_USyd_AUS.py similarity index 87% rename from test/DCEmodels/test_DCEmodels_Patlak_ST_USydAUS.py rename to test/DCEmodels/test_DCEmodels_Patlak_ST_USyd_AUS.py index 1e7635df..b7975716 100644 --- a/test/DCEmodels/test_DCEmodels_Patlak_ST_USydAUS.py +++ b/test/DCEmodels/test_DCEmodels_Patlak_ST_USyd_AUS.py @@ -4,7 +4,7 @@ from time import perf_counter from ..helpers import osipi_parametrize, log_init, log_results from . import DCEmodels_data -from src.original.ST_USydAUS.ModelDictionary import PatlakModel +from src.original.ST_USyd_AUS.ModelDictionary import PatlakModel arg_names = 'label, t_array, C_t_array, cp_aif_array, vp_ref, ps_ref, ' \ 'delay_ref, a_tol_vp, r_tol_vp, a_tol_ps, r_tol_ps, a_tol_delay, ' \ @@ -18,7 +18,8 @@ def setup_module(module): global filename_prefix # we want to change the global variable os.makedirs('./test/results/DCEmodels', exist_ok=True) filename_prefix = 'DCEmodels/TestResults_models' - log_init(filename_prefix, '_ST_USydAus_patlak', ['label', 'time (us)', 'vp_ref', 'ps_ref', 'vp_meas', 'ps_meas']) + log_init(filename_prefix, '_ST_USydAUS_patlak', ['label', 'time (us)', + 'vp_ref', 'ps_ref', 'vp_meas', 'ps_meas']) # Use the test data to generate a parametrize decorator. This causes the following # test to be run for every test case listed in test_data... @@ -45,7 +46,7 @@ def test_ST_USydAUS_Patlak_model(label, t_array, C_t_array, exc_time = 1e6 * (perf_counter() - tic) # measure execution time # log results - log_results(filename_prefix, '_ST_USydAus_patlak', [ + log_results(filename_prefix, '_ST_USydAUS_patlak', [ [label, f"{exc_time:.0f}", vp_ref, ps_ref, vp_meas, ps_meas]]) # run test diff --git a/test/DCEmodels/test_DCEmodels_etofts_LEK_UoEdinburghUK.py b/test/DCEmodels/test_DCEmodels_etofts_LEK_UoEdinburgh_UK.py similarity index 81% rename from test/DCEmodels/test_DCEmodels_etofts_LEK_UoEdinburghUK.py rename to test/DCEmodels/test_DCEmodels_etofts_LEK_UoEdinburgh_UK.py index 69f00e86..36150a1e 100644 --- a/test/DCEmodels/test_DCEmodels_etofts_LEK_UoEdinburghUK.py +++ b/test/DCEmodels/test_DCEmodels_etofts_LEK_UoEdinburgh_UK.py @@ -4,7 +4,7 @@ from time import perf_counter from ..helpers import osipi_parametrize, log_init, log_results from . import DCEmodels_data -from osipi_code_collection.original.LEK_UoEdinburghUK.PharmacokineticModelling.models import ExtKety +from osipi_code_collection.original.LEK_UoEdinburgh_UK.PharmacokineticModelling.models import ExtKety # All tests will use the same arguments and same data... arg_names = 'label, t_array, C_array, ca_array, ta_array, ve_ref, vp_ref, Ktrans_ref, arterial_delay_ref, a_tol_ve, ' \ @@ -19,14 +19,14 @@ def setup_module(module): global filename_prefix # we want to change the global variable os.makedirs('./test/results/DCEmodels', exist_ok=True) filename_prefix = 'DCEmodels/TestResults_models' - log_init(filename_prefix, '_LEK_UoEdinburghUK_etofts', ['label', 'time (us)', 'Ktrans_ref', 've_ref', 'vp_ref', 'delay_ref', 'Ktrans_meas', 've_meas', 'vp_meas', 'delay_meas']) + log_init(filename_prefix, '_LEK_UoEdinburgh_UK_etofts', ['label', 'time (us)', 'Ktrans_ref', 've_ref', 'vp_ref', 'delay_ref', 'Ktrans_meas', 've_meas', 'vp_meas', 'delay_meas']) test_data = (DCEmodels_data.dce_DRO_data_extended_tofts_kety()) # Use the test data to generate a parametrize decorator. This causes the following test to be run for every test case # listed in test_data... @osipi_parametrize(arg_names, test_data, xf_labels=[]) -def test_LEK_UoEdinburghUK_extended_tofts_kety_model(label, t_array, C_array, ca_array, ta_array, ve_ref, vp_ref, +def test_LEK_UoEdinburgh_UK_extended_tofts_kety_model(label, t_array, C_array, ca_array, ta_array, ve_ref, vp_ref, Ktrans_ref, arterial_delay_ref, a_tol_ve, r_tol_ve, a_tol_vp, r_tol_vp, a_tol_Ktrans, r_tol_Ktrans, a_tol_delay, r_tol_delay): # NOTES: @@ -48,7 +48,7 @@ def test_LEK_UoEdinburghUK_extended_tofts_kety_model(label, t_array, C_array, ca arterial_delay_meas = arterial_delay_ref # log results - log_results(filename_prefix, '_LEK_UoEdinburghUK_etofts', [[label, f"{exc_time:.0f}", Ktrans_ref, ve_ref, vp_ref, arterial_delay_ref, Ktrans_meas, ve_meas, vp_meas, arterial_delay_meas]]) + log_results(filename_prefix, '_LEK_UoEdinburgh_UK_etofts', [[label, f"{exc_time:.0f}", Ktrans_ref, ve_ref, vp_ref, arterial_delay_ref, Ktrans_meas, ve_meas, vp_meas, arterial_delay_meas]]) # run test np.testing.assert_allclose([ve_meas], [ve_ref], rtol=r_tol_ve, atol=a_tol_ve) @@ -60,7 +60,7 @@ def test_LEK_UoEdinburghUK_extended_tofts_kety_model(label, t_array, C_array, ca # Use the test data to generate a parametrize decorator. This causes the following test to be run for every test case # listed in test_data... @osipi_parametrize(arg_names, test_data_delay, xf_labels=[]) -def test_LEK_UoEdinburghUK_extended_tofts_kety_model_delay(label, t_array, +def test_LEK_UoEdinburgh_UK_extended_tofts_kety_model_delay(label, t_array, C_array, ca_array, ta_array, ve_ref, vp_ref, Ktrans_ref, arterial_delay_ref, a_tol_ve, r_tol_ve, a_tol_vp, r_tol_vp, a_tol_Ktrans, r_tol_Ktrans, a_tol_delay, r_tol_delay): @@ -81,7 +81,7 @@ def test_LEK_UoEdinburghUK_extended_tofts_kety_model_delay(label, t_array, arterial_delay_meas *= 60 # convert to s # log results - log_results(filename_prefix, '_LEK_UoEdinburghUK_etofts', [[label, f"{exc_time:.0f}", Ktrans_ref, ve_ref, vp_ref, arterial_delay_ref, Ktrans_meas, ve_meas, vp_meas, arterial_delay_meas]]) + log_results(filename_prefix, '_LEK_UoEdinburgh_UK_etofts', [[label, f"{exc_time:.0f}", Ktrans_ref, ve_ref, vp_ref, arterial_delay_ref, Ktrans_meas, ve_meas, vp_meas, arterial_delay_meas]]) # run test np.testing.assert_allclose([ve_meas], [ve_ref], rtol=r_tol_ve, atol=a_tol_ve) diff --git a/test/DCEmodels/test_DCEmodels_etofts_MB_QBI_UoManchesterUK.py b/test/DCEmodels/test_DCEmodels_etofts_MB_QBI_UoManchester_UK.py similarity index 95% rename from test/DCEmodels/test_DCEmodels_etofts_MB_QBI_UoManchesterUK.py rename to test/DCEmodels/test_DCEmodels_etofts_MB_QBI_UoManchester_UK.py index eec0753f..a7500f53 100644 --- a/test/DCEmodels/test_DCEmodels_etofts_MB_QBI_UoManchesterUK.py +++ b/test/DCEmodels/test_DCEmodels_etofts_MB_QBI_UoManchester_UK.py @@ -3,7 +3,7 @@ from time import perf_counter from ..helpers import osipi_parametrize, log_init, log_results from . import DCEmodels_data -from osipi_code_collection.original.MB_QBI_UoManchesterUK.QbiPy.dce_models import tofts_model, dce_aif +from osipi_code_collection.original.MB_QBI_UoManchester_UK.QbiPy.dce_models import tofts_model, dce_aif # All tests will use the same arguments and same data... arg_names = 'label, t_array, C_array, ca_array, ta_array, ve_ref, vp_ref, Ktrans_ref, arterial_delay_ref, a_tol_ve, ' \ diff --git a/test/DCEmodels/test_DCEmodels_etofts_MJT_UoEdinburghUK.py b/test/DCEmodels/test_DCEmodels_etofts_MJT_UoEdinburgh_UK.py similarity index 83% rename from test/DCEmodels/test_DCEmodels_etofts_MJT_UoEdinburghUK.py rename to test/DCEmodels/test_DCEmodels_etofts_MJT_UoEdinburgh_UK.py index 43a37b88..6d3b2d22 100644 --- a/test/DCEmodels/test_DCEmodels_etofts_MJT_UoEdinburghUK.py +++ b/test/DCEmodels/test_DCEmodels_etofts_MJT_UoEdinburgh_UK.py @@ -3,7 +3,7 @@ from time import perf_counter from ..helpers import osipi_parametrize, log_init, log_results from . import DCEmodels_data -from osipi_code_collection.original.MJT_UoEdinburghUK import dce_fit, pk_models, aifs +from osipi_code_collection.original.MJT_UoEdinburgh_UK import dce_fit, pk_models, aifs # All tests will use the same arguments and same data... arg_names = 'label, t_array, C_array, ca_array, ta_array, ve_ref, vp_ref, Ktrans_ref, arterial_delay_ref, a_tol_ve, ' \ @@ -16,14 +16,14 @@ def setup_module(module): global filename_prefix # we want to change the global variable os.makedirs('./test/results/DCEmodels', exist_ok=True) filename_prefix = 'DCEmodels/TestResults_models' - log_init(filename_prefix, '_MJT_UoEdinburghUK_etofts', ['label', 'time (us)', 'Ktrans_ref', 've_ref', 'vp_ref', 'delay_ref', 'Ktrans_meas', 've_meas', 'vp_meas', 'delay_meas']) + log_init(filename_prefix, '_MJT_UoEdinburgh_UK_etofts', ['label', 'time (us)', 'Ktrans_ref', 've_ref', 'vp_ref', 'delay_ref', 'Ktrans_meas', 've_meas', 'vp_meas', 'delay_meas']) test_data = (DCEmodels_data.dce_DRO_data_extended_tofts_kety()) # Use the test data to generate a parametrize decorator. This causes the following # test to be run for every test case listed in test_data... @osipi_parametrize(arg_names, test_data, xf_labels=[]) -def test_MJT_UoEdinburghUK_extended_tofts_kety_model(label, t_array, C_array, ca_array, ta_array, ve_ref, vp_ref, +def test_MJT_UoEdinburgh_UK_extended_tofts_kety_model(label, t_array, C_array, ca_array, ta_array, ve_ref, vp_ref, Ktrans_ref, arterial_delay_ref, a_tol_ve, r_tol_ve, a_tol_vp, r_tol_vp, a_tol_Ktrans, r_tol_Ktrans, a_tol_delay, r_tol_delay): # NOTES: @@ -42,7 +42,7 @@ def test_MJT_UoEdinburghUK_extended_tofts_kety_model(label, t_array, C_array, ca exc_time = 1e6 * (perf_counter() - tic) # measure execution time # log results - log_results(filename_prefix, '_MJT_UoEdinburghUK_etofts', [[label, f"{exc_time:.0f}", Ktrans_ref, ve_ref, vp_ref, + log_results(filename_prefix, '_MJT_UoEdinburgh_UK_etofts', [[label, f"{exc_time:.0f}", Ktrans_ref, ve_ref, vp_ref, arterial_delay_ref, Ktrans_meas, ve_meas, vp_meas, arterial_delay_ref]]) @@ -56,7 +56,7 @@ def test_MJT_UoEdinburghUK_extended_tofts_kety_model(label, t_array, C_array, ca # Use the test data to generate a parametrize decorator. This causes the following # test to be run for every test case listed in test_data... @osipi_parametrize(arg_names, test_data_delay, xf_labels=[]) -def test_MJT_UoEdinburghUK_extended_tofts_kety_model_delay(label, t_array, C_array, ca_array, ta_array, ve_ref, vp_ref, +def test_MJT_UoEdinburgh_UK_extended_tofts_kety_model_delay(label, t_array, C_array, ca_array, ta_array, ve_ref, vp_ref, Ktrans_ref, arterial_delay_ref, a_tol_ve, r_tol_ve, a_tol_vp, r_tol_vp, a_tol_Ktrans, r_tol_Ktrans, a_tol_delay, r_tol_delay): # NOTES: @@ -75,7 +75,7 @@ def test_MJT_UoEdinburghUK_extended_tofts_kety_model_delay(label, t_array, C_arr exc_time = 1e6 * (perf_counter() - tic) # measure execution time # log results - log_results(filename_prefix, '_MJT_UoEdinburghUK_etofts', [[label, f"{exc_time:.0f}", Ktrans_ref, ve_ref, vp_ref, + log_results(filename_prefix, '_MJT_UoEdinburgh_UK_etofts', [[label, f"{exc_time:.0f}", Ktrans_ref, ve_ref, vp_ref, arterial_delay_ref, Ktrans_meas, ve_meas, vp_meas, delay_meas]]) diff --git a/test/DCEmodels/test_DCEmodels_etofts_OGJ_OsloU_NOR.py b/test/DCEmodels/test_DCEmodels_etofts_OGJ_OsloU_NOR.py index 42598a90..463b299c 100644 --- a/test/DCEmodels/test_DCEmodels_etofts_OGJ_OsloU_NOR.py +++ b/test/DCEmodels/test_DCEmodels_etofts_OGJ_OsloU_NOR.py @@ -18,8 +18,10 @@ def setup_module(module): global filename_prefix # we want to change the global variable os.makedirs('./test/results/DCEmodels', exist_ok=True) filename_prefix = 'DCEmodels/TestResults_models' - log_init(filename_prefix, '_OGJ_OsloU_Norway_etofts_LLSQ', ['label', 'time (us)', 'Ktrans_ref', 've_ref', 'vp_ref', 'Ktrans_meas', 've_meas', 'vp_meas']) - log_init(filename_prefix, '_OGJ_OsloU_Norway_etofts_NLLS', ['label', 'time (us)', 'Ktrans_ref', 've_ref', 'vp_ref', 'Ktrans_meas', 've_meas', 'vp_meas']) + log_init(filename_prefix, '_OGJ_OsloU_NOR_etofts_LLSQ', ['label', 'time (' + 'us)', 'Ktrans_ref', 've_ref', 'vp_ref', 'Ktrans_meas', 've_meas', 'vp_meas']) + log_init(filename_prefix, '_OGJ_OsloU_NOR_etofts_NLLS', ['label', 'time (' + 'us)', 'Ktrans_ref', 've_ref', 'vp_ref', 'Ktrans_meas', 've_meas', 'vp_meas']) # Use the test data to generate a parametrize decorator. This causes the following test to be run for every test case @@ -45,7 +47,7 @@ def test_OGJ_OsloU_NOR_extended_tofts_kety_model_llsq(label, t_array, C_array, exc_time = 1e6 * (perf_counter() - tic) # measure execution time # log results - log_results(filename_prefix, '_OGJ_OsloU_Norway_etofts_LLSQ', [ + log_results(filename_prefix, '_OGJ_OsloU_NOR_etofts_LLSQ', [ [label, f"{exc_time:.0f}", Ktrans_ref, ve_ref, vp_ref, Ktrans_meas, ve_meas, vp_meas]]) # run test @@ -75,7 +77,7 @@ def test_OGJ_OsloU_NOR_extended_tofts_kety_model_nlls(label, t_array, C_array, exc_time = 1e6 * (perf_counter() - tic) # measure execution time # log results - log_results(filename_prefix, '_OGJ_OsloU_Norway_etofts_NLLS', [ + log_results(filename_prefix, '_OGJ_OsloU_NOR_etofts_NLLS', [ [label, f"{exc_time:.0f}", Ktrans_ref, ve_ref, vp_ref, Ktrans_meas, ve_meas, vp_meas]]) # run test diff --git a/test/DCEmodels/test_DCEmodels_etofts_OG_MO_AUMC_ICR_RMH_NL_UK.py b/test/DCEmodels/test_DCEmodels_etofts_OG_MO_AUMC_ICR_RMH_NL_UK.py index 95dcedaa..133c4d57 100644 --- a/test/DCEmodels/test_DCEmodels_etofts_OG_MO_AUMC_ICR_RMH_NL_UK.py +++ b/test/DCEmodels/test_DCEmodels_etofts_OG_MO_AUMC_ICR_RMH_NL_UK.py @@ -20,7 +20,8 @@ def setup_module(module): global filename_prefix # we want to change the global variable os.makedirs('./test/results/DCEmodels', exist_ok=True) filename_prefix = 'DCEmodels/TestResults_models' - log_init(filename_prefix, '_OG_MO_AUMC_ICR_RMH_etofts', ['label', 'time (us)', 'Ktrans_ref', 've_ref', 'vp_ref', 'delay_ref', 'Ktrans_meas', 've_meas', 'vp_meas', 'delay_meas']) + log_init(filename_prefix, '_OG_MO_AUMC_ICR_RMH_NL_UK_etofts', ['label', + 'time (us)', 'Ktrans_ref', 've_ref', 'vp_ref', 'delay_ref', 'Ktrans_meas', 've_meas', 'vp_meas', 'delay_meas']) test_data = (DCEmodels_data.dce_DRO_data_extended_tofts_kety()) @@ -64,7 +65,8 @@ def test_OG_MO_AUMC_ICR_RMH_NL_UK_extended_tofts_kety_model(label, t_array, exc_time = 1e6 * (perf_counter() - tic) # measure execution time # log results - log_results(filename_prefix, '_OG_MO_AUMC_ICR_RMH_etofts', [[label, f"{exc_time:.0f}", Ktrans_ref, ve_ref, vp_ref, arterial_delay_ref, Ktrans_meas, ve_meas, vp_meas, arterial_delay_meas]]) + log_results(filename_prefix, '_OG_MO_AUMC_ICR_RMH_NL_UK_etofts', [[label, + f"{exc_time:.0f}", Ktrans_ref, ve_ref, vp_ref, arterial_delay_ref, Ktrans_meas, ve_meas, vp_meas, arterial_delay_meas]]) # run test np.testing.assert_allclose([ve_meas], [ve_ref], rtol=r_tol_ve, atol=a_tol_ve) @@ -112,7 +114,8 @@ def testOG_MO_AUMC_ICR_RMH_NL_UK_extended_tofts_kety_model_delay(label, t_array, exc_time = 1e6 * (perf_counter() - tic) # measure execution time # log results - log_results(filename_prefix, '_OG_MO_AUMC_ICR_RMH_etofts', [[label, f"{exc_time:.0f}", Ktrans_ref, ve_ref, vp_ref, arterial_delay_ref, Ktrans_meas, ve_meas, vp_meas, arterial_delay_meas]]) + log_results(filename_prefix, '_OG_MO_AUMC_ICR_RMH_NL_UK_etofts', [[label, + f"{exc_time:.0f}", Ktrans_ref, ve_ref, vp_ref, arterial_delay_ref, Ktrans_meas, ve_meas, vp_meas, arterial_delay_meas]]) # run test np.testing.assert_allclose([ve_meas], [ve_ref], rtol=r_tol_ve, atol=a_tol_ve) diff --git a/test/DCEmodels/test_DCEmodels_etofts_ST_USydAUS.py b/test/DCEmodels/test_DCEmodels_etofts_ST_USyd_AUS.py similarity index 90% rename from test/DCEmodels/test_DCEmodels_etofts_ST_USydAUS.py rename to test/DCEmodels/test_DCEmodels_etofts_ST_USyd_AUS.py index 79aa8319..a5450a1e 100644 --- a/test/DCEmodels/test_DCEmodels_etofts_ST_USydAUS.py +++ b/test/DCEmodels/test_DCEmodels_etofts_ST_USyd_AUS.py @@ -18,7 +18,8 @@ def setup_module(module): global filename_prefix # we want to change the global variable os.makedirs('./test/results/DCEmodels', exist_ok=True) filename_prefix = 'DCEmodels/TestResults_models' - log_init(filename_prefix, '_ST_USydAus_etofts', ['label', 'time (us)', 'Ktrans_ref', 've_ref', 'vp_ref', 'Ktrans_meas', 've_meas', 'vp_meas']) + log_init(filename_prefix, '_ST_USydAUS_etofts', ['label', 'time (us)', + 'Ktrans_ref', 've_ref', 'vp_ref', 'Ktrans_meas', 've_meas', 'vp_meas']) # Use the test data to generate a parametrize decorator. This causes the following @@ -43,7 +44,7 @@ def testST_USydAUS_extended_tofts_kety_model(label, t_array, C_array, ca_array, exc_time = 1e6 * (perf_counter() - tic) # measure execution time # log results - log_results(filename_prefix, '_ST_USydAus_etofts', [ + log_results(filename_prefix, '_ST_USydAUS_etofts', [ [label, f"{exc_time:.0f}", Ktrans_ref, ve_ref, vp_ref, Ktrans_meas, ve_meas, vp_meas]]) # run test diff --git a/test/DCEmodels/test_DCEmodels_tofts_LEK_UoEdinburghUK.py b/test/DCEmodels/test_DCEmodels_tofts_LEK_UoEdinburgh_UK.py similarity index 85% rename from test/DCEmodels/test_DCEmodels_tofts_LEK_UoEdinburghUK.py rename to test/DCEmodels/test_DCEmodels_tofts_LEK_UoEdinburgh_UK.py index 053c1834..a3133e20 100644 --- a/test/DCEmodels/test_DCEmodels_tofts_LEK_UoEdinburghUK.py +++ b/test/DCEmodels/test_DCEmodels_tofts_LEK_UoEdinburgh_UK.py @@ -4,7 +4,7 @@ from time import perf_counter from ..helpers import osipi_parametrize, log_init, log_results from . import DCEmodels_data -from osipi_code_collection.original.LEK_UoEdinburghUK.PharmacokineticModelling.models import ExtKety, Kety +from osipi_code_collection.original.LEK_UoEdinburgh_UK.PharmacokineticModelling.models import ExtKety, Kety arg_names = 'label, t_array, C_array, ca_array, ta_array, ve_ref, Ktrans_ref, arterial_delay_ref, a_tol_ve, ' \ 'r_tol_ve, a_tol_Ktrans, r_tol_Ktrans, a_tol_delay, r_tol_delay' @@ -16,14 +16,14 @@ def setup_module(module): global filename_prefix # we want to change the global variable os.makedirs('./test/results/DCEmodels', exist_ok=True) filename_prefix = 'DCEmodels/TestResults_models' - log_init(filename_prefix, '_LEK_UoEdinburghUK_tofts', ['label', 'time (us)', 'Ktrans_ref', 've_ref', 'delay_ref', 'Ktrans_meas', 've_meas', 'delay_meas']) + log_init(filename_prefix, '_LEK_UoEdinburgh_UK_tofts', ['label', 'time (us)', 'Ktrans_ref', 've_ref', 'delay_ref', 'Ktrans_meas', 've_meas', 'delay_meas']) # Use the test data to generate a parametrize decorator. This causes the following test to be run for every test case # listed in test_data... test_data = (DCEmodels_data.dce_DRO_data_tofts()) @osipi_parametrize(arg_names, test_data, xf_labels=[]) -def test_LEK_UoEdinburghUK_tofts_model(label, t_array, C_array, ca_array, ta_array, ve_ref, Ktrans_ref, +def test_LEK_UoEdinburgh_UK_tofts_model(label, t_array, C_array, ca_array, ta_array, ve_ref, Ktrans_ref, arterial_delay_ref, a_tol_ve, r_tol_ve, a_tol_Ktrans, r_tol_Ktrans, a_tol_delay, r_tol_delay): # NOTES: @@ -43,7 +43,7 @@ def test_LEK_UoEdinburghUK_tofts_model(label, t_array, C_array, ca_array, ta_arr exc_time = 1e6 * (perf_counter() - tic) # measure execution time # log results - log_results(filename_prefix, '_LEK_UoEdinburghUK_tofts', [ + log_results(filename_prefix, '_LEK_UoEdinburgh_UK_tofts', [ [label, f"{exc_time:.0f}", Ktrans_ref, ve_ref, arterial_delay_ref, Ktrans_meas, ve_meas, arterial_delay_ref]]) # run test @@ -53,7 +53,7 @@ def test_LEK_UoEdinburghUK_tofts_model(label, t_array, C_array, ca_array, ta_arr test_data_delay = (DCEmodels_data.dce_DRO_data_tofts(delay=True)) @osipi_parametrize(arg_names, test_data_delay, xf_labels=[]) -def test_LEK_UoEdinburghUK_tofts_model_delay(label, t_array, C_array, ca_array, +def test_LEK_UoEdinburgh_UK_tofts_model_delay(label, t_array, C_array, ca_array, ta_array, ve_ref, Ktrans_ref, arterial_delay_ref, a_tol_ve, r_tol_ve, a_tol_Ktrans, r_tol_Ktrans, a_tol_delay, r_tol_delay): @@ -74,7 +74,7 @@ def test_LEK_UoEdinburghUK_tofts_model_delay(label, t_array, C_array, ca_array, exc_time = 1e6 * (perf_counter() - tic) # measure execution time # log results - log_results(filename_prefix, '_LEK_UoEdinburghUK_tofts', [ + log_results(filename_prefix, '_LEK_UoEdinburgh_UK_tofts', [ [label, f"{exc_time:.0f}", Ktrans_ref, ve_ref, arterial_delay_ref, Ktrans_meas, ve_meas, arterial_delay_meas]]) # run test diff --git a/test/DCEmodels/test_DCEmodels_tofts_MJT_UoEdinburghUK.py b/test/DCEmodels/test_DCEmodels_tofts_MJT_UoEdinburgh_UK.py similarity index 82% rename from test/DCEmodels/test_DCEmodels_tofts_MJT_UoEdinburghUK.py rename to test/DCEmodels/test_DCEmodels_tofts_MJT_UoEdinburgh_UK.py index 76864ad5..e46e1016 100644 --- a/test/DCEmodels/test_DCEmodels_tofts_MJT_UoEdinburghUK.py +++ b/test/DCEmodels/test_DCEmodels_tofts_MJT_UoEdinburgh_UK.py @@ -3,7 +3,7 @@ from time import perf_counter from ..helpers import osipi_parametrize, log_init, log_results from . import DCEmodels_data -from osipi_code_collection.original.MJT_UoEdinburghUK import dce_fit, pk_models, aifs +from osipi_code_collection.original.MJT_UoEdinburgh_UK import dce_fit, pk_models, aifs arg_names = 'label, t_array, C_array, ca_array, ta_array, ve_ref, Ktrans_ref, arterial_delay_ref, a_tol_ve, ' \ 'r_tol_ve, a_tol_Ktrans,r_tol_Ktrans,a_tol_delay,r_tol_delay ' @@ -15,14 +15,14 @@ def setup_module(module): global filename_prefix # we want to change the global variable os.makedirs('./test/results/DCEmodels', exist_ok=True) filename_prefix = 'DCEmodels/TestResults_models' - log_init(filename_prefix, '_MJT_UoEdinburghUK_tofts', ['label', 'time (us)', 'Ktrans_ref', 've_ref', 'delay_ref', 'Ktrans_meas', 've_meas', 'delay_meas']) + log_init(filename_prefix, '_MJT_UoEdinburgh_UK_tofts', ['label', 'time (us)', 'Ktrans_ref', 've_ref', 'delay_ref', 'Ktrans_meas', 've_meas', 'delay_meas']) test_data = (DCEmodels_data.dce_DRO_data_tofts()) # Use the test data to generate a parametrize decorator. This causes the following # test to be run for every test case listed in test_data... @osipi_parametrize(arg_names, test_data, xf_labels=[]) -def test_MJT_UoEdinburghUK_tofts_model(label, t_array, C_array, ca_array, ta_array, ve_ref, Ktrans_ref, +def test_MJT_UoEdinburgh_UK_tofts_model(label, t_array, C_array, ca_array, ta_array, ve_ref, Ktrans_ref, arterial_delay_ref, a_tol_ve, r_tol_ve, a_tol_Ktrans, r_tol_Ktrans, a_tol_delay, r_tol_delay): # NOTES: @@ -37,7 +37,7 @@ def test_MJT_UoEdinburghUK_tofts_model(label, t_array, C_array, ca_array, ta_arr exc_time = 1e6 * (perf_counter() - tic) # measure execution time # log results - log_results(filename_prefix, '_MJT_UoEdinburghUK_tofts', [ + log_results(filename_prefix, '_MJT_UoEdinburgh_UK_tofts', [ [label, f"{exc_time:.0f}", Ktrans_ref, ve_ref, arterial_delay_ref, Ktrans_meas, ve_meas, arterial_delay_ref]]) # run test @@ -47,7 +47,7 @@ def test_MJT_UoEdinburghUK_tofts_model(label, t_array, C_array, ca_array, ta_arr test_data_delay = (DCEmodels_data.dce_DRO_data_tofts(delay=True)) @osipi_parametrize(arg_names, test_data_delay, xf_labels=[]) -def test_MJT_UoEdinburghUK_tofts_model_delay(label, t_array, C_array, ca_array, ta_array, ve_ref, Ktrans_ref, +def test_MJT_UoEdinburgh_UK_tofts_model_delay(label, t_array, C_array, ca_array, ta_array, ve_ref, Ktrans_ref, arterial_delay_ref, a_tol_ve, r_tol_ve, a_tol_Ktrans, r_tol_Ktrans, a_tol_delay, r_tol_delay): # NOTES: @@ -62,7 +62,7 @@ def test_MJT_UoEdinburghUK_tofts_model_delay(label, t_array, C_array, ca_array, exc_time = 1e6 * (perf_counter() - tic) # measure execution time # log results - log_results(filename_prefix, '_MJT_UoEdinburghUK_tofts', [ + log_results(filename_prefix, '_MJT_UoEdinburgh_UK_tofts', [ [label, f"{exc_time:.0f}", Ktrans_ref, ve_ref, arterial_delay_ref, Ktrans_meas, ve_meas, delay_meas]]) # run test diff --git a/test/DCEmodels/test_DCEmodels_tofts_OGJ_OsloU_NOR.py b/test/DCEmodels/test_DCEmodels_tofts_OGJ_OsloU_NOR.py index 6b355724..d08c3def 100644 --- a/test/DCEmodels/test_DCEmodels_tofts_OGJ_OsloU_NOR.py +++ b/test/DCEmodels/test_DCEmodels_tofts_OGJ_OsloU_NOR.py @@ -17,8 +17,10 @@ def setup_module(module): global filename_prefix # we want to change the global variable os.makedirs('./test/results/DCEmodels', exist_ok=True) filename_prefix = 'DCEmodels/TestResults_models' - log_init(filename_prefix, '_OGJ_OsloU_Norway_tofts_NLLS', ['label', 'time (us)', 'Ktrans_ref', 've_ref', 'Ktrans_meas', 've_meas']) - log_init(filename_prefix, '_OGJ_OsloU_Norway_tofts_LLSQ', ['label', 'time (us)', 'Ktrans_ref', 've_ref', 'Ktrans_meas', 've_meas']) + log_init(filename_prefix, '_OGJ_OsloU_NOR_tofts_NLLS', ['label', + 'time (us)', 'Ktrans_ref', 've_ref', 'Ktrans_meas', 've_meas']) + log_init(filename_prefix, '_OGJ_OsloU_NOR_tofts_LLSQ', ['label', 'time (' + 'us)', 'Ktrans_ref', 've_ref', 'Ktrans_meas', 've_meas']) # Use the test data to generate a parametrize decorator. This causes the following test to be run for every test case @@ -42,7 +44,7 @@ def test_OGJ_OsloU_NOR_tofts_model_llsq(label, t_array, C_array, ca_array, exc_time = 1e6 * (perf_counter() - tic) # measure execution time # log results - log_results(filename_prefix, '_OGJ_OsloU_Norway_tofts_LLSQ', [ + log_results(filename_prefix, '_OGJ_OsloU_NOR_tofts_LLSQ', [ [label, f"{exc_time:.0f}", Ktrans_ref, ve_ref, Ktrans_meas, ve_meas]]) # run test @@ -69,7 +71,7 @@ def test_OGJ_OsloU_NOR_tofts_model_nlls(label, t_array, C_array, ca_array, exc_time = 1e6 * (perf_counter() - tic) # measure execution time # log results - log_results(filename_prefix, '_OGJ_OsloU_Norway_tofts_NLLS', [ + log_results(filename_prefix, '_OGJ_OsloU_NOR_tofts_NLLS', [ [label, f"{exc_time:.0f}", Ktrans_ref, ve_ref, Ktrans_meas, ve_meas]]) # run test diff --git a/test/DCEmodels/test_DCEmodels_tofts_ST_USydAUS.py b/test/DCEmodels/test_DCEmodels_tofts_ST_USyd_AUS.py similarity index 89% rename from test/DCEmodels/test_DCEmodels_tofts_ST_USydAUS.py rename to test/DCEmodels/test_DCEmodels_tofts_ST_USyd_AUS.py index 430b8a50..822c6958 100644 --- a/test/DCEmodels/test_DCEmodels_tofts_ST_USydAUS.py +++ b/test/DCEmodels/test_DCEmodels_tofts_ST_USyd_AUS.py @@ -17,7 +17,8 @@ def setup_module(module): global filename_prefix # we want to change the global variable os.makedirs('./test/results/DCEmodels', exist_ok=True) filename_prefix = 'DCEmodels/TestResults_models' - log_init(filename_prefix, '_ST_USydAus_tofts', ['label', 'time (us)', 'Ktrans_ref', 've_ref', 'Ktrans_meas', 've_meas']) + log_init(filename_prefix, '_ST_USydAUS_tofts', ['label', 'time (us)', + 'Ktrans_ref', 've_ref', 'Ktrans_meas', 've_meas']) # Use the test data to generate a parametrize decorator. This causes the following @@ -42,7 +43,7 @@ def testST_USydAUS_tofts_model(label, t_array, C_array, ca_array, ta_array, ve_r exc_time = 1e6 * (perf_counter() - tic) # measure execution time # log results - log_results(filename_prefix, '_ST_USydAus_tofts', [ + log_results(filename_prefix, '_ST_USydAUS_tofts', [ [label, f"{exc_time:.0f}", Ktrans_ref, ve_ref, Ktrans_meas, ve_meas]]) # run test diff --git a/test/DSCmodels/test_DSCmodels_LcurveReg_SR_TBG_BNIPhoenixUSA.py b/test/DSCmodels/test_DSCmodels_LcurveReg_SR_TBG_BNIPhoenix_USA.py similarity index 90% rename from test/DSCmodels/test_DSCmodels_LcurveReg_SR_TBG_BNIPhoenixUSA.py rename to test/DSCmodels/test_DSCmodels_LcurveReg_SR_TBG_BNIPhoenix_USA.py index fc90fb7c..67e1df91 100644 --- a/test/DSCmodels/test_DSCmodels_LcurveReg_SR_TBG_BNIPhoenixUSA.py +++ b/test/DSCmodels/test_DSCmodels_LcurveReg_SR_TBG_BNIPhoenix_USA.py @@ -3,8 +3,8 @@ from time import perf_counter from ..helpers import osipi_parametrize, log_init, log_results from . import DSCmodels_data -from src.original.SR_TBG_BNIPhoenixUSA.AIFDeconvolution.AIF_deconvolution import AIFdeconvolution -from src.original.SR_TBG_BNIPhoenixUSA.DSCparameters.DSC_parameters import DSCparameters +from src.original.SR_TBG_BNIPhoenix_USA.AIFDeconvolution.AIF_deconvolution import AIFdeconvolution +from src.original.SR_TBG_BNIPhoenix_USA.DSCparameters.DSC_parameters import DSCparameters # All tests will use the same arguments and same data... arg_names = 'label, C_tis, C_aif, tr, cbv_ref, cbf_ref,' \ diff --git a/test/PopulationAIF_DCE/test_popAIF_Parker_MB_QBI_UoManchesterUK.py b/test/PopulationAIF_DCE/test_popAIF_Parker_MB_QBI_UoManchester_UK.py similarity index 85% rename from test/PopulationAIF_DCE/test_popAIF_Parker_MB_QBI_UoManchesterUK.py rename to test/PopulationAIF_DCE/test_popAIF_Parker_MB_QBI_UoManchester_UK.py index d0400ef7..f5cb004c 100644 --- a/test/PopulationAIF_DCE/test_popAIF_Parker_MB_QBI_UoManchesterUK.py +++ b/test/PopulationAIF_DCE/test_popAIF_Parker_MB_QBI_UoManchester_UK.py @@ -3,7 +3,7 @@ import numpy as np from time import perf_counter from ..helpers import osipi_parametrize, log_init, log_results -import osipi_code_collection.original.MB_QBI_UoManchesterUK.QbiPy.dce_models.dce_aif as dce_aif +import osipi_code_collection.original.MB_QBI_UoManchester_UK.QbiPy.dce_models.dce_aif as dce_aif from . import popAIF_data @@ -20,13 +20,13 @@ def setup_module(module): global filename_prefix # we want to change the global variable os.makedirs('./test/results/PopulationAIF_DCE', exist_ok=True) filename_prefix = 'PopulationAIF_DCE/TestResults_PopAIF' - log_init(filename_prefix, '_Parker_AIF_MB_QBI_UoManchesterUK', ['label', 'time (us)', 'time_ref', 'aif_ref', 'cb_measured']) + log_init(filename_prefix, '_Parker_AIF_MB_QBI_UoManchester_UK', ['label', 'time (us)', 'time_ref', 'aif_ref', 'cb_measured']) # Use the test data to generate a parametrize decorator. This causes the following # test to be run for every test case listed in test_data... # In the following test, we specify 5 cases that are expected to fail as this function expects the delay to be specified according to the temp resolution @osipi_parametrize(arg_names, test_data, xf_labels=[]) -def test_Parker_AIF_MB_QBI_UoManchesterUK(label, time, cb_ref_values, delay, a_tol, r_tol): +def test_Parker_AIF_MB_QBI_UoManchester_UK(label, time, cb_ref_values, delay, a_tol, r_tol): # prepare input data # time array is expected in minutes, so no changes needed. @@ -42,6 +42,6 @@ def test_Parker_AIF_MB_QBI_UoManchesterUK(label, time, cb_ref_values, delay, a_t row_data = [] for t, ref, meas in zip(time, cb_ref_values, aif_delay[0,]): row_data.append([label, f"{exc_time:.0f}", t*60, ref, meas]) - log_results(filename_prefix, '_Parker_AIF_MB_QBI_UoManchesterUK', row_data) + log_results(filename_prefix, '_Parker_AIF_MB_QBI_UoManchester_UK', row_data) np.testing.assert_allclose([aif_delay[0,]], [cb_ref_values], rtol=r_tol, atol=a_tol) diff --git a/test/PopulationAIF_DCE/test_popAIF_Parker_MJT_EdinburghUK.py b/test/PopulationAIF_DCE/test_popAIF_Parker_MJT_Edinburgh_UK.py similarity index 82% rename from test/PopulationAIF_DCE/test_popAIF_Parker_MJT_EdinburghUK.py rename to test/PopulationAIF_DCE/test_popAIF_Parker_MJT_Edinburgh_UK.py index cb79f565..22ba7f67 100644 --- a/test/PopulationAIF_DCE/test_popAIF_Parker_MJT_EdinburghUK.py +++ b/test/PopulationAIF_DCE/test_popAIF_Parker_MJT_Edinburgh_UK.py @@ -2,7 +2,7 @@ import numpy as np from time import perf_counter from ..helpers import osipi_parametrize, log_init, log_results -import osipi_code_collection.original.MJT_UoEdinburghUK.aifs as aifs +import osipi_code_collection.original.MJT_UoEdinburgh_UK.aifs as aifs from . import popAIF_data @@ -19,13 +19,13 @@ def setup_module(module): global filename_prefix # we want to change the global variable os.makedirs('./test/results/PopulationAIF_DCE', exist_ok=True) filename_prefix = 'PopulationAIF_DCE/TestResults_PopAIF' - log_init(filename_prefix, '_Parker_AIF_MJT_EdinburghUK', ['label', 'time (us)', 'time_ref', 'aif_ref', 'cb_measured']) + log_init(filename_prefix, '_Parker_AIF_MJT_Edinburgh_UK', ['label', 'time (us)', 'time_ref', 'aif_ref', 'cb_measured']) # Use the test data to generate a parametrize decorator. This causes the following # test to be run for every test case listed in test_data... # In the following test, we specify 5 cases that are expected to fail as this function expects the delay to be specified according to the temp resolution @osipi_parametrize(arg_names, test_data, xf_labels=[]) -def test_Parker_AIF_MJT_EdinburghUK(label, time, cb_ref_values, delay, a_tol, r_tol): +def test_Parker_AIF_MJT_Edinburgh_UK(label, time, cb_ref_values, delay, a_tol, r_tol): # prepare input data time = time*60 # time array is expected in seconds @@ -43,6 +43,6 @@ def test_Parker_AIF_MJT_EdinburghUK(label, time, cb_ref_values, delay, a_tol, r_ row_data = [] for t, ref, meas in zip(time, cb_ref_values, c_ap): row_data.append([label, f"{exc_time:.0f}", t, ref, meas]) - log_results(filename_prefix, '_Parker_AIF_MJT_EdinburghUK', row_data) + log_results(filename_prefix, '_Parker_AIF_MJT_Edinburgh_UK', row_data) np.testing.assert_allclose([c_ap], [cb_ref_values], rtol=r_tol, atol=a_tol) diff --git a/test/PopulationAIF_DCE/test_popAIF_Parker_ST_SydneyAUS.py b/test/PopulationAIF_DCE/test_popAIF_Parker_ST_Sydney_AUS.py similarity index 84% rename from test/PopulationAIF_DCE/test_popAIF_Parker_ST_SydneyAUS.py rename to test/PopulationAIF_DCE/test_popAIF_Parker_ST_Sydney_AUS.py index b101c9ca..d5f01578 100644 --- a/test/PopulationAIF_DCE/test_popAIF_Parker_ST_SydneyAUS.py +++ b/test/PopulationAIF_DCE/test_popAIF_Parker_ST_Sydney_AUS.py @@ -20,13 +20,14 @@ def setup_module(module): global filename_prefix # we want to change the global variable os.makedirs('./test/results/PopulationAIF_DCE', exist_ok=True) filename_prefix = 'PopulationAIF_DCE/TestResults_PopAIF' - log_init(filename_prefix, '_Parker_AIF_ST_SydneyAus', ['label', 'time (us)', 'time_ref', 'aif_ref', 'cb_measured']) + log_init(filename_prefix, '_Parker_AIF_ST_Sydney_AUS', ['label', 'time (' + 'us)', 'time_ref', 'aif_ref', 'cb_measured']) # Use the test data to generate a parametrize decorator. This causes the following # test to be run for every test case listed in test_data. # some test data fails as this code uses a shift of the original AIF in time and doesn't recalculate the values based on the new time array @osipi_parametrize(arg_names, test_data, xf_labels=['delay_5.0s','delay_10.0s','delay_31.0s','delay_2.0s']) -def test_Parker_AIF_ST_SydneyAUS(label, time, cb_ref_values, delay, a_tol, +def test_Parker_AIF_ST_Sydney_AUS(label, time, cb_ref_values, delay, a_tol, r_tol): # prepare input data @@ -40,6 +41,6 @@ def test_Parker_AIF_ST_SydneyAUS(label, time, cb_ref_values, delay, a_tol, row_data = [] for t, ref, meas in zip(time, cb_ref_values, AIF_P): row_data.append([label, f"{exc_time:.0f}", t, ref, meas]) - log_results(filename_prefix, '_Parker_AIF_ST_SydneyAus', row_data) + log_results(filename_prefix, '_Parker_AIF_ST_Sydney_AUS', row_data) np.testing.assert_allclose([AIF_P], [cb_ref_values], rtol=r_tol, atol=a_tol) diff --git a/test/PopulationAIF_DCE/test_popAIF_preclinical_ST_SydneyAUS.py b/test/PopulationAIF_DCE/test_popAIF_preclinical_ST_Sydney_AUS.py similarity index 84% rename from test/PopulationAIF_DCE/test_popAIF_preclinical_ST_SydneyAUS.py rename to test/PopulationAIF_DCE/test_popAIF_preclinical_ST_Sydney_AUS.py index b1f8031c..4256c8f0 100644 --- a/test/PopulationAIF_DCE/test_popAIF_preclinical_ST_SydneyAUS.py +++ b/test/PopulationAIF_DCE/test_popAIF_preclinical_ST_Sydney_AUS.py @@ -20,12 +20,12 @@ def setup_module(module): global filename_prefix # we want to change the global variable os.makedirs('./test/results/PopulationAIF_DCE', exist_ok=True) filename_prefix = 'PopulationAIF_DCE/TestResults_PopAIF' - log_init(filename_prefix, '_preclinical_AIF_ST_SydneyAus', ['label', 'time (us)', 'time_ref', 'aif_ref', 'cb_measured']) + log_init(filename_prefix, '_preclinical_AIF_ST_Sydney_AUS', ['label', 'time (us)', 'time_ref', 'aif_ref', 'cb_measured']) # Use the test data to generate a parametrize decorator. This causes the following # test to be run for every test case listed in test_data... @osipi_parametrize(arg_names, test_data, xf_labels=[]) -def test_preclinical_AIF_ST_SydneyAUS(label, time, cb_ref_values, delay, +def test_preclinical_AIF_ST_Sydney_AUS(label, time, cb_ref_values, delay, a_tol, r_tol): # prepare input data @@ -38,6 +38,6 @@ def test_preclinical_AIF_ST_SydneyAUS(label, time, cb_ref_values, delay, row_data = [] for t, ref, meas in zip(time, cb_ref_values, AIF_P): row_data.append([label, f"{exc_time:.0f}", t, ref, meas]) - log_results(filename_prefix, '_preclinical_AIF_ST_SydneyAus', row_data) + log_results(filename_prefix, '_preclinical_AIF_ST_Sydney_AUS', row_data) np.testing.assert_allclose([AIF_P], [cb_ref_values], rtol=r_tol, atol=a_tol) diff --git a/test/SI_to_Conc/test_SI2Conc_LEK_EdinburghUK.py b/test/SI_to_Conc/test_SI2Conc_LEK_Edinburgh_UK.py old mode 100755 new mode 100644 similarity index 89% rename from test/SI_to_Conc/test_SI2Conc_LEK_EdinburghUK.py rename to test/SI_to_Conc/test_SI2Conc_LEK_Edinburgh_UK.py index ea7fec64..7b6f10d2 --- a/test/SI_to_Conc/test_SI2Conc_LEK_EdinburghUK.py +++ b/test/SI_to_Conc/test_SI2Conc_LEK_Edinburgh_UK.py @@ -4,7 +4,7 @@ from time import perf_counter from ..helpers import osipi_parametrize, log_init, log_results from . import SI2Conc_data -from osipi_code_collection.original.LEK_UoEdinburghUK.SignalToConcentration import SI2Conc +from osipi_code_collection.original.LEK_UoEdinburgh_UK.SignalToConcentration import SI2Conc # All tests will use the same arguments and same data... @@ -23,7 +23,7 @@ def setup_module(module): # Use the test data to generate a parametrize decorator. This causes the following # test to be run for every test case listed in test_data... @osipi_parametrize(arg_names, test_data, xf_labels = []) -def test_LEK_UoEdinburghUK_SI2Conc(label, fa, tr, T1base, BLpts, r1, s_array, conc_array, a_tol, r_tol): +def test_LEK_UoEdinburgh_UK_SI2Conc(label, fa, tr, T1base, BLpts, r1, s_array, conc_array, a_tol, r_tol): # Note: the first signal value is not used for baseline estimation, # and the first C value is not logged or assessed diff --git a/test/SI_to_Conc/test_SI2Conc_MB_QBI_UoManchesterUK.py b/test/SI_to_Conc/test_SI2Conc_MB_QBI_UoManchester_UK.py similarity index 94% rename from test/SI_to_Conc/test_SI2Conc_MB_QBI_UoManchesterUK.py rename to test/SI_to_Conc/test_SI2Conc_MB_QBI_UoManchester_UK.py index 0a49dfe5..7b0ee103 100644 --- a/test/SI_to_Conc/test_SI2Conc_MB_QBI_UoManchesterUK.py +++ b/test/SI_to_Conc/test_SI2Conc_MB_QBI_UoManchester_UK.py @@ -4,7 +4,7 @@ from time import perf_counter from ..helpers import osipi_parametrize, log_init, log_results from . import SI2Conc_data -from osipi_code_collection.original.MB_QBI_UoManchesterUK.QbiPy.dce_models.tissue_concentration import signal_to_concentration +from osipi_code_collection.original.MB_QBI_UoManchester_UK.QbiPy.dce_models.tissue_concentration import signal_to_concentration diff --git a/test/SI_to_Conc/test_SI2Conc_MJT_UoEdinburghUK.py b/test/SI_to_Conc/test_SI2Conc_MJT_UoEdinburgh_UK.py similarity index 86% rename from test/SI_to_Conc/test_SI2Conc_MJT_UoEdinburghUK.py rename to test/SI_to_Conc/test_SI2Conc_MJT_UoEdinburgh_UK.py index 62fd1209..9b85cae6 100644 --- a/test/SI_to_Conc/test_SI2Conc_MJT_UoEdinburghUK.py +++ b/test/SI_to_Conc/test_SI2Conc_MJT_UoEdinburgh_UK.py @@ -3,10 +3,10 @@ from time import perf_counter from ..helpers import osipi_parametrize, log_init, log_results from . import SI2Conc_data -from osipi_code_collection.original.MJT_UoEdinburghUK.signal_models import SPGR -from osipi_code_collection.original.MJT_UoEdinburghUK.relaxivity import CRLinear -from osipi_code_collection.original.MJT_UoEdinburghUK.dce_fit import SigToEnh -from osipi_code_collection.original.MJT_UoEdinburghUK.dce_fit import EnhToConc, EnhToConcSPGR +from osipi_code_collection.original.MJT_UoEdinburgh_UK.signal_models import SPGR +from osipi_code_collection.original.MJT_UoEdinburgh_UK.relaxivity import CRLinear +from osipi_code_collection.original.MJT_UoEdinburgh_UK.dce_fit import SigToEnh +from osipi_code_collection.original.MJT_UoEdinburgh_UK.dce_fit import EnhToConc, EnhToConcSPGR # All tests will use the same arguments and same data... @@ -26,7 +26,7 @@ def setup_module(module): # Use the test data to generate a parametrize decorator. This causes the following # test to be run for every test case listed in test_data... @osipi_parametrize(arg_names, test_data, xf_labels = []) -def test_MJT_UoEdinburghUK_sig_to_conc_num(label, fa, tr, T1base, BLpts, r1, s_array, conc_array, a_tol, r_tol): +def test_MJT_UoEdinburgh_UK_sig_to_conc_num(label, fa, tr, T1base, BLpts, r1, s_array, conc_array, a_tol, r_tol): # Note: the first signal value is not used for baseline estimation, # and the first C value is not logged or assessed @@ -68,7 +68,7 @@ def test_MJT_UoEdinburghUK_sig_to_conc_num(label, fa, tr, T1base, BLpts, r1, s_a @osipi_parametrize(arg_names, test_data, xf_labels = []) -def test_MJT_UoEdinburghUK_sig_to_conc(label, fa, tr, T1base, BLpts, r1, s_array, conc_array, a_tol, r_tol): +def test_MJT_UoEdinburgh_UK_sig_to_conc(label, fa, tr, T1base, BLpts, r1, s_array, conc_array, a_tol, r_tol): # Note: the first signal value is not used for baseline estimation, # and the first C value is not logged or assessed diff --git a/test/SI_to_Conc/test_SI2Conc_OG_MO_AUMC_ICR_RMH_NL_UK.py b/test/SI_to_Conc/test_SI2Conc_OG_MO_AUMC_ICR_RMH_NL_UK.py index 1b5fde3b..9d82ab45 100644 --- a/test/SI_to_Conc/test_SI2Conc_OG_MO_AUMC_ICR_RMH_NL_UK.py +++ b/test/SI_to_Conc/test_SI2Conc_OG_MO_AUMC_ICR_RMH_NL_UK.py @@ -20,7 +20,8 @@ def setup_module(module): global filename_prefix # we want to change the global variable os.makedirs('./test/results/SI_to_Conc', exist_ok=True) filename_prefix = 'SI_to_Conc/TestResults_SI2Conc' - log_init(filename_prefix, '_OG_MO_AUMC_ICR_RMH',['label', 'time (us)', 'conc_ref', 'conc_meas']) + log_init(filename_prefix, '_OG_MO_AUMC_ICR_RMH_NL_UK',['label', 'time (' + 'us)', 'conc_ref', 'conc_meas']) # Use the test data to generate a parametrize decorator. This causes the following @@ -55,7 +56,7 @@ def test_OG_MO_AUMC_ICR_RMH_NL_UK_SI2Conc(label, fa, tr, T1base, row_data = [] for ref, meas in zip(conc_array[1:], conc_curve[1:]): row_data.append([label, f"{exc_time:.0f}", ref, meas]) - log_results(filename_prefix, '_OG_MO_AUMC_ICR_RMH', row_data) + log_results(filename_prefix, '_OG_MO_AUMC_ICR_RMH_NL_UK', row_data) np.testing.assert_allclose( conc_curve[1:], conc_array[1:], rtol=r_tol, atol=a_tol ) diff --git a/test/SI_to_Conc/test_SI2Conc_ST_USydAUS.py b/test/SI_to_Conc/test_SI2Conc_ST_USyd_AUS.py similarity index 90% rename from test/SI_to_Conc/test_SI2Conc_ST_USydAUS.py rename to test/SI_to_Conc/test_SI2Conc_ST_USyd_AUS.py index 34542ec9..88424402 100644 --- a/test/SI_to_Conc/test_SI2Conc_ST_USydAUS.py +++ b/test/SI_to_Conc/test_SI2Conc_ST_USyd_AUS.py @@ -18,7 +18,8 @@ def setup_module(module): global filename_prefix # we want to change the global variable os.makedirs('./test/results/SI_to_Conc', exist_ok=True) filename_prefix = 'SI_to_Conc/TestResults_SI2Conc' - log_init(filename_prefix, '_ST_USydAus', ['label', 'time (us)', 'conc_ref', 'conc_meas']) + log_init(filename_prefix, '_ST_USydAUS', ['label', 'time (us)', + 'conc_ref', 'conc_meas']) # Use the test data to generate a parametrize decorator. This causes the following @@ -45,7 +46,7 @@ def test_ST_USydAUS_signals2conc(label, fa, tr, T1base, BLpts, r1, s_array, conc row_data = [] for ref, meas in zip(conc_array, conc_curve): row_data.append([label, f"{exc_time:.0f}", ref, meas]) - log_results(filename_prefix, '_ST_USydAus', row_data) + log_results(filename_prefix, '_ST_USydAUS', row_data) np.testing.assert_allclose( [conc_curve], [conc_array], rtol=r_tol, atol=a_tol ) diff --git a/test/T1_mapping/test_t1_MJT_EdinburghUK.py b/test/T1_mapping/test_t1_MJT_Edinburgh_UK.py similarity index 68% rename from test/T1_mapping/test_t1_MJT_EdinburghUK.py rename to test/T1_mapping/test_t1_MJT_Edinburgh_UK.py index c22546cb..059ea8a3 100644 --- a/test/T1_mapping/test_t1_MJT_EdinburghUK.py +++ b/test/T1_mapping/test_t1_MJT_Edinburgh_UK.py @@ -4,7 +4,7 @@ from time import perf_counter from ..helpers import osipi_parametrize, log_init, log_results from . import t1_data -from osipi_code_collection.original.MJT_UoEdinburghUK.t1_fit import VFALinear, VFANonLinear, VFA2Points +from osipi_code_collection.original.MJT_UoEdinburgh_UK.t1_fit import VFALinear, VFANonLinear, VFA2Points # All tests will use the same arguments and same data... @@ -22,15 +22,15 @@ def setup_module(module): global filename_prefix # we want to change the global variable os.makedirs('./test/results/T1_mapping', exist_ok=True) filename_prefix = 'T1_mapping/TestResults_T1mapping' - log_init(filename_prefix, '_MJT_EdinburghUK_t1_VFA_nonlin', ['label', 'time (us)', 'r1_ref', 'r1_measured']) - log_init(filename_prefix, '_MJT_EdinburghUK_t1_VFA_lin', ['label', 'time (us)', 'r1_ref', 'r1_measured']) - log_init(filename_prefix, '_MJT_EdinburghUK_t1_VFA_2fa', ['label', 'time (us)', 'r1_ref', 'r1_measured']) + log_init(filename_prefix, '_MJT_Edinburgh_UK_t1_VFA_nonlin', ['label', 'time (us)', 'r1_ref', 'r1_measured']) + log_init(filename_prefix, '_MJT_Edinburgh_UK_t1_VFA_lin', ['label', 'time (us)', 'r1_ref', 'r1_measured']) + log_init(filename_prefix, '_MJT_Edinburgh_UK_t1_VFA_2fa', ['label', 'time (us)', 'r1_ref', 'r1_measured']) # Use the test data to generate a parametrize decorator. This causes the following # test to be run for every test case listed in test_data... @osipi_parametrize(arg_names, test_data, xf_labels = []) -def test_MJT_EdinburghUK_t1_VFA_nonlin(label, fa_array, tr_array, s_array, r1_ref, s0_ref, a_tol, r_tol): +def test_MJT_Edinburgh_UK_t1_VFA_nonlin(label, fa_array, tr_array, s_array, r1_ref, s0_ref, a_tol, r_tol): # NOTES: # prepare input data @@ -41,14 +41,14 @@ def test_MJT_EdinburghUK_t1_VFA_nonlin(label, fa_array, tr_array, s_array, r1_re [s0_nonlin_meas, t1_nonlin_meas] = VFANonLinear(fa_array,tr).proc(s_array) exc_time = 1e6 * (perf_counter() - tic) r1_nonlin_meas = 1./t1_nonlin_meas - log_results(filename_prefix, '_MJT_EdinburghUK_t1_VFA_nonlin', [[label, f"{exc_time:.0f}", r1_ref, r1_nonlin_meas]]) # log results + log_results(filename_prefix, '_MJT_Edinburgh_UK_t1_VFA_nonlin', [[label, f"{exc_time:.0f}", r1_ref, r1_nonlin_meas]]) # log results np.testing.assert_allclose([r1_nonlin_meas], [r1_ref], rtol=r_tol, atol=a_tol) # In the following test, we specify 1 case that is expected to fail... @osipi_parametrize(arg_names, test_data, xf_labels = ['Pat5_voxel5_prostaat']) -def test_MJT_EdinburghUK_t1_VFA_lin(label, fa_array, tr_array, s_array, r1_ref, s0_ref, a_tol, r_tol): +def test_MJT_Edinburgh_UK_t1_VFA_lin(label, fa_array, tr_array, s_array, r1_ref, s0_ref, a_tol, r_tol): # NOTES: # Expected fails: 1 low-SNR prostate voxel @@ -60,13 +60,13 @@ def test_MJT_EdinburghUK_t1_VFA_lin(label, fa_array, tr_array, s_array, r1_ref, [s0_lin_meas, t1_lin_meas] = VFALinear(fa_array,tr).proc(s_array) exc_time = 1e6 * (perf_counter() - tic) r1_lin_meas = 1./t1_lin_meas - log_results(filename_prefix, '_MJT_EdinburghUK_t1_VFA_lin', [[label, f"{exc_time:.0f}", r1_ref, r1_lin_meas]]) # log results + log_results(filename_prefix, '_MJT_Edinburgh_UK_t1_VFA_lin', [[label, f"{exc_time:.0f}", r1_ref, r1_lin_meas]]) # log results np.testing.assert_allclose([r1_lin_meas], [r1_ref], rtol=r_tol, atol=a_tol) # In the following test, we specify 1 case that is expected to fail... @osipi_parametrize(arg_names, test_data, xf_labels = ['Pat5_voxel5_prostaat']) -def test_MJT_EdinburghUK_t1_VFA_2fa(label, fa_array, tr_array, s_array, r1_ref, s0_ref, a_tol, r_tol): +def test_MJT_Edinburgh_UK_t1_VFA_2fa(label, fa_array, tr_array, s_array, r1_ref, s0_ref, a_tol, r_tol): # NOTES: # Expected fails: 1 low-SNR prostate voxel @@ -79,6 +79,6 @@ def test_MJT_EdinburghUK_t1_VFA_2fa(label, fa_array, tr_array, s_array, r1_ref, s_array[-1]])) exc_time = 1e6 * (perf_counter() - tic) r1_2fa_meas = 1./t1_2fa_meas - log_results(filename_prefix, '_MJT_EdinburghUK_t1_VFA_2fa', [[label, f"{exc_time:.0f}", r1_ref, r1_2fa_meas]]) # + log_results(filename_prefix, '_MJT_Edinburgh_UK_t1_VFA_2fa', [[label, f"{exc_time:.0f}", r1_ref, r1_2fa_meas]]) # # log results np.testing.assert_allclose([r1_2fa_meas], [r1_ref], rtol=r_tol, atol=a_tol) \ No newline at end of file diff --git a/test/T1_mapping/test_t1_OG_MO_AUMC_ICR_RMH_NL_UK.py b/test/T1_mapping/test_t1_OG_MO_AUMC_ICR_RMH_NL_UK.py index 94239a5a..2107f579 100644 --- a/test/T1_mapping/test_t1_OG_MO_AUMC_ICR_RMH_NL_UK.py +++ b/test/T1_mapping/test_t1_OG_MO_AUMC_ICR_RMH_NL_UK.py @@ -22,8 +22,10 @@ def setup_module(module): global filename_prefix # we want to change the global variable os.makedirs('./test/results/T1_mapping', exist_ok=True) filename_prefix = 'T1_mapping/TestResults_T1mapping' - log_init(filename_prefix, '_OG_MO_AUMC_ICR_RHM_t1_VFA_2fa', ['label', 'time (us)', 'r1_ref', 'r1_measured']) - log_init(filename_prefix, '_OG_MO_AUMC_ICR_RHM_t1_VFA_nonlin', ['label', 'time (us)', 'r1_ref', 'r1_measured']) + log_init(filename_prefix, '_OG_MO_AUMC_ICR_RHM_NL_UK_t1_VFA_2fa', ['label', + 'time (us)', 'r1_ref', 'r1_measured']) + log_init(filename_prefix, '_OG_MO_AUMC_ICR_RHM_NL_UK_t1_VFA_nonlin', + ['label', 'time (us)', 'r1_ref', 'r1_measured']) # Use the test data to generate a parametrize decorator. This causes the following @@ -46,7 +48,8 @@ def test_OG_MO_AUMC_ICR_RMH_NL_UK_t1_VFA_2fa(label, fa_array, tr_array, tic = perf_counter() r1_2fa_meas = R1_two_fas(s_array_trimmed,fa_array_rad,tr)[0] exc_time = 1e6 * (perf_counter() - tic) - log_results(filename_prefix, '_OG_MO_AUMC_ICR_RHM_t1_VFA_2fa', [[label, f"{exc_time:.0f}", r1_ref, r1_2fa_meas]]) # log results to csv + log_results(filename_prefix, '_OG_MO_AUMC_ICR_RHM_NL_UK_t1_VFA_2fa', + [[label, f"{exc_time:.0f}", r1_ref, r1_2fa_meas]]) # log results to csv np.testing.assert_allclose( [r1_2fa_meas], [r1_ref], rtol=r_tol, atol=a_tol ) @@ -66,5 +69,6 @@ def test_OG_MO_AUMC_ICR_RMH_NL_UK_t1_VFA(label, fa_array, tr_array, s_array, tic = perf_counter() r1_meas = 1/R1_VFA(s_array, fa_array_rad, tr) exc_time = 1e6 * (perf_counter() - tic) - log_results(filename_prefix, '_OG_MO_AUMC_ICR_RHM_t1_VFA_nonlin', [[label, f"{exc_time:.0f}", r1_ref, r1_meas]]) # log results to csv + log_results(filename_prefix, '_OG_MO_AUMC_ICR_RHM_NL_UK_t1_VFA_nonlin', + [[label, f"{exc_time:.0f}", r1_ref, r1_meas]]) # log results to csv np.testing.assert_allclose([r1_meas], [r1_ref], rtol=r_tol, atol=a_tol) diff --git a/test/T1_mapping/test_t1_ST_SydneyAUS.py b/test/T1_mapping/test_t1_ST_Sydney_AUS.py similarity index 72% rename from test/T1_mapping/test_t1_ST_SydneyAUS.py rename to test/T1_mapping/test_t1_ST_Sydney_AUS.py index 996ad8a3..dac3e5d1 100644 --- a/test/T1_mapping/test_t1_ST_SydneyAUS.py +++ b/test/T1_mapping/test_t1_ST_Sydney_AUS.py @@ -22,13 +22,15 @@ def setup_module(module): global filename_prefix # we want to change the global variable os.makedirs('./test/results/T1_mapping', exist_ok=True) filename_prefix = 'T1_mapping/TestResults_T1mapping' - log_init(filename_prefix, '_ST_SydneyAus_t1_VFA_nonlin', ['label', 'time (us)', 'r1_ref', 'r1_measured']) - log_init(filename_prefix, '_ST_SydneyAus_t1_VFA_lin', ['label', 'time (us)', 'r1_ref', 'r1_measured']) + log_init(filename_prefix, '_ST_Sydney_AUS_t1_VFA_nonlin', ['label', 'time (' + 'us)', 'r1_ref', 'r1_measured']) + log_init(filename_prefix, '_ST_Sydney_AUS_t1_VFA_lin', ['label', 'time (' + 'us)', 'r1_ref', 'r1_measured']) # Use the test data to generate a parametrize decorator. This causes the following # test to be run for every test case listed in test_data... @osipi_parametrize(arg_names, test_data, xf_labels = []) -def test_ST_SydneyAUS_t1_VFA_nonlin(label, fa_array, tr_array, s_array, +def test_ST_Sydney_AUS_t1_VFA_nonlin(label, fa_array, tr_array, s_array, r1_ref, s0_ref, a_tol, r_tol): # NOTES: @@ -40,14 +42,15 @@ def test_ST_SydneyAUS_t1_VFA_nonlin(label, fa_array, tr_array, s_array, [s0_nonlin_meas, t1_nonlin_meas] = VFAT1mapping(fa_array, s_array, tr, method='nonlinear') exc_time = 1e6 * (perf_counter() - tic) r1_nonlin_meas = 1000./t1_nonlin_meas # convert T1 (ms) to R1 (/s) - log_results(filename_prefix, '_ST_SydneyAus_t1_VFA_nonlin', [[label, f"{exc_time:.0f}", r1_ref, r1_nonlin_meas]]) # log results to csv + log_results(filename_prefix, '_ST_Sydney_AUS_t1_VFA_nonlin', [[label, + f"{exc_time:.0f}", r1_ref, r1_nonlin_meas]]) # log results to csv np.testing.assert_allclose([r1_nonlin_meas], [r1_ref], rtol=r_tol, atol=a_tol) # In the following test, we specify 1 case that is expected to fail... @osipi_parametrize(arg_names, test_data, xf_labels = ['Pat5_voxel5_prostaat']) -def test_ST_SydneyAUS_t1_VFA_lin(label, fa_array, tr_array, s_array, r1_ref, +def test_ST_Sydney_AUS_t1_VFA_lin(label, fa_array, tr_array, s_array, r1_ref, s0_ref, a_tol, r_tol): # NOTES: # Signal is scaled to prevent multiple test failures for prostate test cases. @@ -64,5 +67,6 @@ def test_ST_SydneyAUS_t1_VFA_lin(label, fa_array, tr_array, s_array, r1_ref, [s0_lin_meas, t1_lin_meas] = VFAT1mapping(fa_array, s_array, tr, method='linear') exc_time = 1e6 * (perf_counter() - tic) r1_lin_meas = 1000./t1_lin_meas # convert T1 (ms) to R1 (/s) - log_results(filename_prefix, '_ST_SydneyAus_t1_VFA_lin', [[label, f"{exc_time:.0f}", r1_ref, r1_lin_meas]]) # log results to csv + log_results(filename_prefix, '_ST_Sydney_AUS_t1_VFA_lin', [[label, + f"{exc_time:.0f}", r1_ref, r1_lin_meas]]) # log results to csv np.testing.assert_allclose([r1_lin_meas], [r1_ref], rtol=r_tol, atol=a_tol) diff --git a/test/T1_mapping/test_t1_ZA_McGill_CAN.py b/test/T1_mapping/test_t1_ZA_McGill_CAN.py index dbb6443b..f865d2ad 100644 --- a/test/T1_mapping/test_t1_ZA_McGill_CAN.py +++ b/test/T1_mapping/test_t1_ZA_McGill_CAN.py @@ -22,8 +22,9 @@ def setup_module(module): global filename_prefix # we want to change the global variable filename_prefix = 'T1_mapping/TestResults_T1mapping' os.makedirs('./test/results/T1_mapping', exist_ok=True) - log_init(filename_prefix, '_mcgill_t1_novifast', ['label', 'time (us)', 'r1_ref', 'r1_measured']) - log_init(filename_prefix, '_mcgill_t1_VFA_lin', ['label', 'time (us)', 'r1_ref', 'r1_measured']) + log_init(filename_prefix, '_ZA_McGill_CAN_t1_novifast', ['label', + 'time (us)', 'r1_ref', 'r1_measured']) + log_init(filename_prefix, '_ZA_McGill_CAN_t1_VFA_lin', ['label', 'time (us)', 'r1_ref', 'r1_measured']) # Use the test data to generate a parametrize decorator. This causes the following # test to be run for every test case listed in test_data... @@ -64,7 +65,7 @@ def test_ZA_McGill_CAN_t1_VFA_lin(label, fa_array, tr_array, s_array, exc_time = 1e6 * (perf_counter() - tic) r1_lin_meas = 1./t1_lin_meas - log_results(filename_prefix, '_mcgill_t1_VFA_lin', [[label, f"{exc_time:.0f}", r1_ref, r1_lin_meas]]) # log results + log_results(filename_prefix, '_ZA_McGill_CAN_t1_VFA_lin', [[label, f"{exc_time:.0f}", r1_ref, r1_lin_meas]]) # log results np.testing.assert_allclose( [r1_lin_meas], [r1_ref], rtol=r_tol, atol=a_tol ) # testing diff --git a/test/results-meta.json b/test/results-meta.json index 1c85efdf..099433c8 100644 --- a/test/results-meta.json +++ b/test/results-meta.json @@ -8,21 +8,21 @@ }, { "path": "../test/results/T1_mapping", - "filename": "TestResults_T1mapping_MJT_EdinburghUK_t1_VFA_lin.csv", + "filename": "TestResults_T1mapping_MJT_Edinburgh_UK_t1_VFA_lin.csv", "category": "T1mapping", "method": "linear", "author": "MJT_UoEdinburgh_UK" }, { "path": "../test/results/T1_mapping", - "filename": "TestResults_T1mapping_MJT_EdinburghUK_t1_VFA_2fa.csv", + "filename": "TestResults_T1mapping_MJT_Edinburgh_UK_t1_VFA_2fa.csv", "category": "T1mapping", "method": "two-FA", "author": "MJT_UoEdinburgh_UK" }, { "path": "../test/results/T1_mapping", - "filename": "TestResults_T1mapping_ST_SydneyAus_t1_VFA_lin.csv", + "filename": "TestResults_T1mapping_ST_Sydney_AUS_t1_VFA_lin.csv", "category": "T1mapping", "method": "linear", "author": "ST_USyd_Aus" @@ -44,14 +44,14 @@ }, { "path": "../test/results/T1_mapping", - "filename": "TestResults_T1mapping_MJT_EdinburghUK_t1_VFA_nonlin.csv", + "filename": "TestResults_T1mapping_MJT_Edinburgh_UK_t1_VFA_nonlin.csv", "category": "T1mapping", "method": "nonlinear", "author": "MJT_UoEdinburgh_UK" }, { "path": "../test/results/T1_mapping", - "filename": "TestResults_T1mapping_ST_SydneyAus_t1_VFA_nonlin.csv", + "filename": "TestResults_T1mapping_ST_Sydney_AUS_t1_VFA_nonlin.csv", "category": "T1mapping", "method": "nonlinear", "author": "ST_USyd_Aus" @@ -114,17 +114,17 @@ }, { "path": "../test/results/PopulationAIF_DCE", - "filename": "TestResults_PopAIF_Parker_AIF_MJT_EdinburghUK.csv", + "filename": "TestResults_PopAIF_Parker_AIF_MJT_Edinburgh_UK.csv", "category": "PopulationAIF", "method": "Parker", "author": "MJT_UoEdinburgh_UK" }, { "path": "../test/results/PopulationAIF_DCE", - "filename": "TestResults_PopAIF_Parker_AIF_MB_QBI_UoManchesterUK.csv", + "filename": "TestResults_PopAIF_Parker_AIF_MB_QBI_UoManchester_UK.csv", "category": "PopulationAIF", "method": "Parker", - "author": "MB_QBI_UoManchesterUK" + "author": "MB_QBI_UoManchester_UK" }, { "path": "../test/results/PopulationAIF_DCE", @@ -135,7 +135,7 @@ }, { "path": "../test/results/PopulationAIF_DCE", - "filename": "TestResults_PopAIF_Parker_AIF_ST_SydneyAus.csv", + "filename": "TestResults_PopAIF_Parker_AIF_ST_Sydney_AUS.csv", "category": "PopulationAIF", "method": "Parker", "author": "ST_USyd_Aus" @@ -149,7 +149,7 @@ }, { "path": "../test/results/PopulationAIF_DCE", - "filename": "TestResults_PopAIF_preclinical_AIF_ST_SydneyAus.csv", + "filename": "TestResults_PopAIF_preclinical_AIF_ST_Sydney_AUS.csv", "category": "PopulationAIF", "method": "preclinical", "author": "ST_USyd_Aus" @@ -163,35 +163,35 @@ }, { "path": "../test/results/DCEmodels", - "filename": "TestResults_models_LEK_UoEdinburghUK_etofts.csv", + "filename": "TestResults_models_LEK_UoEdinburgh_UK_etofts.csv", "category": "DCEmodels", "method": "etofts", "author": "LEK_UoEdinburgh_UK" }, { "path": "../test/results/DCEmodels", - "filename": "TestResults_models_LEK_UoEdinburghUK_patlak.csv", + "filename": "TestResults_models_LEK_UoEdinburgh_UK_patlak.csv", "category": "DCEmodels", "method": "patlak", "author": "LEK_UoEdinburgh_UK" }, { "path": "../test/results/DCEmodels", - "filename": "TestResults_models_LEK_UoEdinburghUK_tofts.csv", + "filename": "TestResults_models_LEK_UoEdinburgh_UK_tofts.csv", "category": "DCEmodels", "method": "tofts", "author": "LEK_UoEdinburgh_UK" }, { "path": "../test/results/DCEmodels", - "filename": "TestResults_models_LEK_UoEdinburghUK_2CUM.csv", + "filename": "TestResults_models_LEK_UoEdinburgh_UK_2CUM.csv", "category": "DCEmodels", "method": "2CUM", "author": "LEK_UoEdinburgh_UK" }, { "path": "../test/results/DCEmodels", - "filename": "TestResults_models_LEK_UoEdinburghUK_2CXM.csv", + "filename": "TestResults_models_LEK_UoEdinburgh_UK_2CXM.csv", "category": "DCEmodels", "method": "2CXM", "author": "LEK_UoEdinburgh_UK" @@ -205,49 +205,49 @@ }, { "path": "../test/results/DCEmodels", - "filename": "TestResults_models_MB_QBI_UoManchesterUK_2CXM.csv", + "filename": "TestResults_models_MB_QBI_UoManchester_UK_2CXM.csv", "category": "DCEmodels", "method": "2CXM", "author": "MB_QBI_UoManchester" }, { "path": "../test/results/DCEmodels", - "filename": "TestResults_models_MJT_UoEdinburghUK_2CUM.csv", + "filename": "TestResults_models_MJT_UoEdinburgh_UK_2CUM.csv", "category": "DCEmodels", "method": "2CUM", "author": "MJT_UoEdinburgh_UK" }, { "path": "../test/results/DCEmodels", - "filename": "TestResults_models_MJT_UoEdinburghUK_2CXM.csv", + "filename": "TestResults_models_MJT_UoEdinburgh_UK_2CXM.csv", "category": "DCEmodels", "method": "2CXM", "author": "MJT_UoEdinburgh_UK" }, { "path": "../test/results/DCEmodels", - "filename": "TestResults_models_MJT_UoEdinburghUK_etofts.csv", + "filename": "TestResults_models_MJT_UoEdinburgh_UK_etofts.csv", "category": "DCEmodels", "method": "etofts", "author": "MJT_UoEdinburgh_UK" }, { "path": "../test/results/DCEmodels", - "filename": "TestResults_models_MJT_UoEdinburghUK_patlak.csv", + "filename": "TestResults_models_MJT_UoEdinburgh_UK_patlak.csv", "category": "DCEmodels", "method": "patlak", "author": "MJT_UoEdinburgh_UK" }, { "path": "../test/results/DCEmodels", - "filename": "TestResults_models_MJT_UoEdinburghUK_patlak_llsq.csv", + "filename": "TestResults_models_MJT_UoEdinburgh_UK_patlak_llsq.csv", "category": "DCEmodels", "method": "patlak", "author": "MJT_UoEdinburgh_UK_llsq" }, { "path": "../test/results/DCEmodels", - "filename": "TestResults_models_MJT_UoEdinburghUK_tofts.csv", + "filename": "TestResults_models_MJT_UoEdinburgh_UK_tofts.csv", "category": "DCEmodels", "method": "tofts", "author": "MJT_UoEdinburgh_UK"