Implement Philips+GE related spherical harmonics conventions (#498)

* Start adding Philips to the spherical harmonics

* Add dcm2niic to the bin dir

* Fix syntax

* Add to dcm2bids and remove development mode from windows installation

* Add wildcard for fm2d2 sequence

* Add Philips to spherical harmonics basis functions

* Add build folder to git-ignore

* Use the mask to set transparency rather than 0 values

* Update spherical harmonics for ge and philips, update dcm2bids config file

* Correctly output the calculated correction

* Update dcm2bids, remove coordinate origin shift

* Update BIDS config file with EPI and T1w sequences

* Touch ups and fix tests

* Bug fix and PEP improvement

* Add test for ScannerCoil

.gitignore

@@ -5,6 +5,7 @@
 .pytest_cache/
 .ipynb_checkpoints/
 .vscode/
+build/
 
 # Project's data
 testing_data

installer/windows_install.bat

@@ -42,7 +42,7 @@ REM Installing Shimming Toolbox
 copy "%ST_SOURCE_FILES%\config\dcm2bids.json" "%ST_DIR%\dcm2bids.json" || goto error
 
 cd "%ST_SOURCE_FILES%"
-"%ST_DIR%\%PYTHON_DIR%\python.exe" -m pip install -e ".[docs,dev]" --no-warn-script-location || goto error
+"%ST_DIR%\%PYTHON_DIR%\python.exe" -m pip install . --no-warn-script-location || goto error
 
 REM Create launchers for Shimming Toolbox
 set "BIN_DIR=bin"
@@ -52,6 +52,17 @@ for %%f in ("%ST_DIR%\%PYTHON_DIR%\Scripts\st_*.*") do (
 	copy "%%f" "%ST_DIR%\%BIN_DIR%" || goto error
 )
 
+REM Copy dcm2niix to the bin directory, there are 2 places it might be
+set "PATH_DCM2NIIX=%ST_DIR%\%PYTHON_DIR%\Library\bin\dcm2niix.exe"
+if exist "%PATH_DCM2NIIX%" (copy "%PATH_DCM2NIIX%" "%ST_DIR%\%BIN_DIR%" || goto error) else (
+    set "PATH_DCM2NIIX=%ST_DIR%\%PYTHON_DIR%\Scripts\dcm2niix.exe"
+    if exist "%PATH_DCM2NIIX%" (copy "%PATH_DCM2NIIX%" "%ST_DIR%\%BIN_DIR%" || goto error) else (
+        echo "dcm2niix.exe not found"
+        goto error
+    )
+)
+
+
 REM Add scripts to the User's path
 for /F "skip=2 tokens=2,*" %%A in ('reg.exe query "HKEY_CURRENT_USER\Environment" /v path') do set "OLD_PATH=%%B"
 REM If OLD_PATH is not an empty string

shimmingtoolbox/coils/coil.py

@@ -6,9 +6,8 @@
 import numpy as np
 from typing import Tuple
 
-from shimmingtoolbox.coils.spher_harm_basis import siemens_basis, ge_basis
+from shimmingtoolbox.coils.spher_harm_basis import siemens_basis, ge_basis, philips_basis, SHIM_CS
 from shimmingtoolbox.coils.coordinates import generate_meshgrid
-from shimmingtoolbox.shim.shim_utils import shim_cs
 
 logger = logging.getLogger(__name__)
 
@@ -131,8 +130,8 @@ def __init__(self, dim_volume, affine, constraints, orders, manufacturer=""):
         self.orders = orders
 
         manufacturer = manufacturer.upper()
-        if manufacturer in shim_cs:
-            self.coord_system = shim_cs[manufacturer.upper()]
+        if manufacturer in SHIM_CS:
+            self.coord_system = SHIM_CS[manufacturer.upper()]
         else:
             logger.warning(f"Unknown manufacturer {manufacturer}, assuming RAS")
             self.coord_system = 'RAS'
@@ -167,6 +166,9 @@ def _create_coil_profile(self, dim, manufacturer=None):
             elif manufacturer == 'GE':
                 profile_orders = ge_basis(mesh1, mesh2, mesh3, orders=tuple(temp_orders),
                                           shim_cs=self.coord_system)
+            elif manufacturer == 'PHILIPS':
+                profile_orders = philips_basis(mesh1, mesh2, mesh3, orders=tuple(temp_orders),
+                                               shim_cs=self.coord_system)
             else:
                 logger.warning(f"{manufacturer} manufacturer not implemented. Outputting in Hz, uT/m, uT/m^2 for order "
                                f"0, 1 and 2 respectively")

shimmingtoolbox/coils/create_coil_profiles.py

@@ -9,6 +9,7 @@
 logger = logging.getLogger(__name__)
 TOLERANCE = 0.001
 
+
 def create_coil_profiles(fnames_fmaps, list_currents):
     """ Create coil profiles from fieldmaps