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TST: PARREC image with varying slope / intercept
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Test with ArrayProxy API.
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@matthew-brett
matthew-brett committed Nov 20, 2014
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129 changes: 129 additions & 0 deletions nibabel/tests/data/phantom_varscale.PAR
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# === DATA DESCRIPTION FILE ======================================================
#
# CAUTION - Investigational device.
# Limited by Federal Law to investigational use.
#
# Dataset name: E:\\Export\phantom_EPI_asc_CLEAR_2_1
#
# CLINICAL TRYOUT Research image export tool V4.2
#
# === GENERAL INFORMATION ========================================================
#
. Patient name : phantom
. Examination name : Konvertertest
. Protocol name : EPI_asc CLEAR
. Examination date/time : 2014.02.14 / 09:00:57
. Series Type : Image MRSERIES
. Acquisition nr : 2
. Reconstruction nr : 1
. Scan Duration [sec] : 14
. Max. number of cardiac phases : 1
. Max. number of echoes : 1
. Max. number of slices/locations : 9
. Max. number of dynamics : 3
. Max. number of mixes : 1
. Patient position : Head First Supine
. Preparation direction : Anterior-Posterior
. Technique : FEEPI
. Scan resolution (x, y) : 64 39
. Scan mode : MS
. Repetition time [ms] : 2000.000
. FOV (ap,fh,rl) [mm] : 240.000 70.000 240.000
. Water Fat shift [pixels] : 11.050
. Angulation midslice(ap,fh,rl)[degr]: -13.265 0.000 0.000
. Off Centre midslice(ap,fh,rl) [mm] : 2.508 30.339 -16.032
. Flow compensation <0=no 1=yes> ? : 0
. Presaturation <0=no 1=yes> ? : 0
. Phase encoding velocity [cm/sec] : 0.000000 0.000000 0.000000
. MTC <0=no 1=yes> ? : 0
. SPIR <0=no 1=yes> ? : 1
. EPI factor <0,1=no EPI> : 39
. Dynamic scan <0=no 1=yes> ? : 1
. Diffusion <0=no 1=yes> ? : 0
. Diffusion echo time [ms] : 0.0000
. Max. number of diffusion values : 1
. Max. number of gradient orients : 1
. Number of label types <0=no ASL> : 0
#
# === PIXEL VALUES =============================================================
# PV = pixel value in REC file, FP = floating point value, DV = displayed value on console
# RS = rescale slope, RI = rescale intercept, SS = scale slope
# DV = PV * RS + RI FP = DV / (RS * SS)
#
# === IMAGE INFORMATION DEFINITION =============================================
# The rest of this file contains ONE line per image, this line contains the following information:
#
# slice number (integer)
# echo number (integer)
# dynamic scan number (integer)
# cardiac phase number (integer)
# image_type_mr (integer)
# scanning sequence (integer)
# index in REC file (in images) (integer)
# image pixel size (in bits) (integer)
# scan percentage (integer)
# recon resolution (x y) (2*integer)
# rescale intercept (float)
# rescale slope (float)
# scale slope (float)
# window center (integer)
# window width (integer)
# image angulation (ap,fh,rl in degrees ) (3*float)
# image offcentre (ap,fh,rl in mm ) (3*float)
# slice thickness (in mm ) (float)
# slice gap (in mm ) (float)
# image_display_orientation (integer)
# slice orientation ( TRA/SAG/COR ) (integer)
# fmri_status_indication (integer)
# image_type_ed_es (end diast/end syst) (integer)
# pixel spacing (x,y) (in mm) (2*float)
# echo_time (float)
# dyn_scan_begin_time (float)
# trigger_time (float)
# diffusion_b_factor (float)
# number of averages (integer)
# image_flip_angle (in degrees) (float)
# cardiac frequency (bpm) (integer)
# minimum RR-interval (in ms) (integer)
# maximum RR-interval (in ms) (integer)
# TURBO factor <0=no turbo> (integer)
# Inversion delay (in ms) (float)
# diffusion b value number (imagekey!) (integer)
# gradient orientation number (imagekey!) (integer)
# contrast type (string)
# diffusion anisotropy type (string)
# diffusion (ap, fh, rl) (3*float)
# label type (ASL) (imagekey!) (integer)
#
# === IMAGE INFORMATION ==========================================================
# sl ec dyn ph ty idx pix scan% rec size (re)scale window angulation offcentre thick gap info spacing echo dtime ttime diff avg flip freq RR-int turbo delay b grad cont anis diffusion L.ty

1 1 1 1 0 2 0 16 62 64 64 -0.69352 0.65184 4.78462e-003 1070 1860 -13.26 -0.00 -0.00 2.51 -0.81 -8.69 6.000 2.000 0 1 0 2 3.750 3.750 30.00 0.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
2 1 1 1 0 2 1 16 62 64 64 -0.28395 0.18528 5.01287e-003 1122 1951 -13.26 -0.00 -0.00 2.51 6.98 -10.53 6.000 2.000 0 1 0 2 3.750 3.750 30.00 0.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
3 1 1 1 0 2 2 16 62 64 64 0.60964 0.48545 3.20504e-003 1137 1977 -13.26 -0.00 -0.00 2.51 14.77 -12.36 6.000 2.000 0 1 0 2 3.750 3.750 30.00 0.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
4 1 1 1 0 2 3 16 62 64 64 0.23940 0.58869 5.70364e-003 1217 2116 -13.26 -0.00 -0.00 2.51 22.55 -14.20 6.000 2.000 0 1 0 2 3.750 3.750 30.00 0.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
5 1 1 1 0 2 4 16 62 64 64 -0.56774 0.54425 4.19357e-003 1216 2113 -13.26 -0.00 -0.00 2.51 30.34 -16.03 6.000 2.000 0 1 0 2 3.750 3.750 30.00 0.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
6 1 1 1 0 2 5 16 62 64 64 0.84933 0.61451 4.51471e-003 1141 1983 -13.26 -0.00 -0.00 2.51 38.13 -17.87 6.000 2.000 0 1 0 2 3.750 3.750 30.00 0.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
7 1 1 1 0 2 6 16 62 64 64 -0.23580 2.07194 4.81163e-003 1119 1945 -13.26 -0.00 -0.00 2.51 45.91 -19.70 6.000 2.000 0 1 0 2 3.750 3.750 30.00 0.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
8 1 1 1 0 2 7 16 62 64 64 -0.45610 1.75542 3.01393e-003 1097 1907 -13.26 -0.00 -0.00 2.51 53.70 -21.54 6.000 2.000 0 1 0 2 3.750 3.750 30.00 0.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
9 1 1 1 0 2 8 16 62 64 64 -0.33958 0.41352 3.31281e-003 1146 1991 -13.26 -0.00 -0.00 2.51 61.49 -23.37 6.000 2.000 0 1 0 2 3.750 3.750 30.00 0.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
1 1 2 1 0 2 9 16 62 64 64 -0.50054 0.02978 3.02487e-003 1071 1863 -13.26 -0.00 -0.00 2.51 -0.81 -8.69 6.000 2.000 0 1 0 2 3.750 3.750 30.00 2.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
2 1 2 1 0 2 10 16 62 64 64 1.09595 2.68028 4.32900e-003 1123 1953 -13.26 -0.00 -0.00 2.51 6.98 -10.53 6.000 2.000 0 1 0 2 3.750 3.750 30.00 2.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
3 1 2 1 0 2 11 16 62 64 64 0.66260 -0.01198 5.25907e-003 1135 1973 -13.26 -0.00 -0.00 2.51 14.77 -12.36 6.000 2.000 0 1 0 2 3.750 3.750 30.00 2.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
4 1 2 1 0 2 12 16 62 64 64 0.49692 0.62467 3.65960e-003 1209 2101 -13.26 -0.00 -0.00 2.51 22.55 -14.20 6.000 2.000 0 1 0 2 3.750 3.750 30.00 2.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
5 1 2 1 0 2 13 16 62 64 64 -0.81913 0.05637 2.96656e-003 1215 2113 -13.26 -0.00 -0.00 2.51 30.34 -16.03 6.000 2.000 0 1 0 2 3.750 3.750 30.00 2.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
6 1 2 1 0 2 14 16 62 64 64 -0.46862 0.88504 5.71452e-003 1145 1990 -13.26 -0.00 -0.00 2.51 38.13 -17.87 6.000 2.000 0 1 0 2 3.750 3.750 30.00 2.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
7 1 2 1 0 2 15 16 62 64 64 0.24446 3.78608 4.86407e-003 1119 1945 -13.26 -0.00 -0.00 2.51 45.91 -19.70 6.000 2.000 0 1 0 2 3.750 3.750 30.00 2.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
8 1 2 1 0 2 16 16 62 64 64 0.07351 -1.06477 2.57365e-003 1093 1899 -13.26 -0.00 -0.00 2.51 53.70 -21.54 6.000 2.000 0 1 0 2 3.750 3.750 30.00 2.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
9 1 2 1 0 2 17 16 62 64 64 -1.52431 2.45537 5.97195e-003 1150 1999 -13.26 -0.00 -0.00 2.51 61.49 -23.37 6.000 2.000 0 1 0 2 3.750 3.750 30.00 2.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
1 1 3 1 0 2 18 16 62 64 64 0.74747 0.98210 4.98308e-003 1070 1860 -13.26 -0.00 -0.00 2.51 -0.81 -8.69 6.000 2.000 0 1 0 2 3.750 3.750 30.00 4.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
2 1 3 1 0 2 19 16 62 64 64 -0.15021 0.52770 3.56176e-003 1125 1955 -13.26 -0.00 -0.00 2.51 6.98 -10.53 6.000 2.000 0 1 0 2 3.750 3.750 30.00 4.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
3 1 3 1 0 2 20 16 62 64 64 1.68669 0.46589 4.71663e-003 1135 1973 -13.26 -0.00 -0.00 2.51 14.77 -12.36 6.000 2.000 0 1 0 2 3.750 3.750 30.00 4.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
4 1 3 1 0 2 21 16 62 64 64 0.51405 0.88194 4.60270e-003 1211 2105 -13.26 -0.00 -0.00 2.51 22.55 -14.20 6.000 2.000 0 1 0 2 3.750 3.750 30.00 4.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
5 1 3 1 0 2 22 16 62 64 64 -1.47991 2.03474 4.01615e-003 1218 2118 -13.26 -0.00 -0.00 2.51 30.34 -16.03 6.000 2.000 0 1 0 2 3.750 3.750 30.00 4.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
6 1 3 1 0 2 23 16 62 64 64 -1.66364 3.21846 4.54139e-003 1143 1987 -13.26 -0.00 -0.00 2.51 38.13 -17.87 6.000 2.000 0 1 0 2 3.750 3.750 30.00 4.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
7 1 3 1 0 2 24 16 62 64 64 0.60690 -0.41266 2.81800e-003 1120 1947 -13.26 -0.00 -0.00 2.51 45.91 -19.70 6.000 2.000 0 1 0 2 3.750 3.750 30.00 4.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
8 1 3 1 0 2 25 16 62 64 64 1.01725 0.91765 3.19469e-003 1093 1901 -13.26 -0.00 -0.00 2.51 53.70 -21.54 6.000 2.000 0 1 0 2 3.750 3.750 30.00 4.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
9 1 3 1 0 2 26 16 62 64 64 0.79204 1.65725 3.95777e-003 1151 2001 -13.26 -0.00 -0.00 2.51 61.49 -23.37 6.000 2.000 0 1 0 2 3.750 3.750 30.00 4.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1

# === END OF DATA DESCRIPTION FILE ===============================================
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29 changes: 29 additions & 0 deletions nibabel/tests/test_parrec.py
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Expand Up @@ -15,6 +15,7 @@
vol_is_full, PARRECImage, PARRECArrayProxy)
from ..openers import Opener
from ..fileholders import FileHolder
from ..volumeutils import array_from_file

from numpy.testing import (assert_almost_equal,
assert_array_equal)
Expand All @@ -40,6 +41,9 @@
V4_PAR = pjoin(DATA_PATH, 'phantom_fake_v4.PAR')
# Fake V4.1
V41_PAR = pjoin(DATA_PATH, 'phantom_fake_v4_1.PAR')
# Fake varying scaling
VARY_PAR = pjoin(DATA_PATH, 'phantom_varscale.PAR')
VARY_REC = pjoin(DATA_PATH, 'phantom_varscale.REC')
# Affine as we determined it mid-2014
AN_OLD_AFFINE = np.array(
[[-3.64994708, 0., 1.83564171, 123.66276611],
Expand Down Expand Up @@ -554,3 +558,28 @@ def test_bitpix():
for pix_size in (24, 32):
hdr_defs['image pixel size'] = pix_size
assert_raises(PARRECError, PARRECHeader, HDR_INFO, hdr_defs)


def test_varying_scaling():
# Check the algorithm works as expected for varying scaling
img = PARRECImage.load(VARY_REC)
rec_shape = (64, 64, 27)
with open(VARY_REC, 'rb') as fobj:
arr = array_from_file(rec_shape, '<i2', fobj)
img_defs = img.header.image_defs
slopes = img_defs['rescale slope']
inters = img_defs['rescale intercept']
sc_slopes = img_defs['scale slope']
# Check dv scaling
scaled_arr = arr.astype(np.float64)
for i in range(arr.shape[2]):
scaled_arr[:, :, i] *= slopes[i]
scaled_arr[:, :, i] += inters[i]
assert_almost_equal(np.reshape(scaled_arr, img.shape, order='F'),
img.get_data(), 9)
# Check fp scaling
for i in range(arr.shape[2]):
scaled_arr[:, :, i] /= (slopes[i] * sc_slopes[i])
dv_img = PARRECImage.load(VARY_REC, scaling='fp')
assert_almost_equal(np.reshape(scaled_arr, img.shape, order='F'),
dv_img.get_data(), 9)
26 changes: 16 additions & 10 deletions nibabel/tests/test_proxy_api.py
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Original file line number Diff line number Diff line change
Expand Up @@ -63,8 +63,8 @@
from ..tmpdirs import InTemporaryDirectory

from .test_api_validators import ValidateAPI
from .test_parrec import EG_REC, VARY_REC

from .test_parrec import EG_PAR, EG_REC

def _some_slicers(shape):
ndim = len(shape)
Expand Down Expand Up @@ -375,15 +375,21 @@ def validate_header_isolated(self, pmaker, params):

class TestPARRECAPI(_TestProxyAPI):

def obj_params(self):
img = parrec.load(EG_PAR)
def _func_dict(self, rec_name):
img = parrec.load(rec_name)
arr_out = img.get_data()
def eg_func():
img = parrec.load(EG_PAR)
prox = parrec.PARRECArrayProxy(EG_REC, img.header, 'dv')
fobj = open(EG_REC, 'rb')
img = parrec.load(rec_name)
prox = parrec.PARRECArrayProxy(rec_name,
img.header,
scaling='dv')
fobj = open(rec_name, 'rb')
return prox, fobj, img.header
yield (eg_func,
dict(shape = (64, 64, 9, 3),
dtype_out=np.float64,
arr_out=arr_out))
return (eg_func,
dict(shape = img.shape,
dtype_out=np.float64,
arr_out=arr_out))

def obj_params(self):
yield self._func_dict(EG_REC)
yield self._func_dict(VARY_REC)

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