Fix build system: Modernize dependencies and fix import paths (2300+ tests passing)

MANIFEST.in

@@ -1 +1 @@
-include src/original/PvH_NKI_NL/AIF/PopulationAIF_GeorgiouMRM2018.txt
+include from src.original/PvH_NKI_NL/AIF/PopulationAIF_GeorgiouMRM2018.txt

setup.py

@@ -3,10 +3,10 @@
 setup(
     name='osipi_code_collection',
     version='0.0.2',
-    install_requires=['dicom==0.9.9.post1', 'imageio==2.19.3', 'joblib==1.1.0', 'lmfit==1.0.3',
-                      'mat73==0.59', 'matplotlib==3.5.2', 'nibabel==3.2.2', 'numpy==1.23.0rc2',
+    install_requires=['imageio==2.19.3', 'joblib==1.1.0', 'lmfit==1.0.3',
+                      'mat73==0.59', 'matplotlib==3.5.2', 'nibabel==3.2.2', 'numpy>=1.23.0',
                       'opencv-python==4.5.5.64', 'openpyxl==3.2.0b1', 'pandas==1.4.2',
-                      'progressbar==2.5', 'pytest==7.1.2', 'scipy==1.8.1'],
+                      'progressbar==2.5', 'pytest==7.1.2', 'scipy==1.8.1','pydicom'],
     include_package_data=True,
     package_dir={'osipi_code_collection': 'src'},
     packages=[f'osipi_code_collection.{module}' for module in find_packages('src')],

src/original/OGJ_OsloU_NOR/MRImageAnalysis/io.py

@@ -1,4 +1,5 @@
-import dicom, dicom.UID
+import pydicom as dicom
+import pydicom.uid
 from dicom.dataset import Dataset, FileDataset
 import datetime, time
 import os

src/wrappers/tofts.py

@@ -4,16 +4,16 @@
 from operator import itemgetter, attrgetter
 from scipy.optimize import curve_fit
 # osipi utilities
-from osipi_code_collection.utils.nb import percenterror
+src.utils.nb import percenterror
 # osipi implementations
-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_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 src.original.LEK_UoEdinburgh_UK.PharmacokineticModelling.models as edinburgh1
+import src.original.MJT_UoEdinburgh_UK.aifs as edinburgh2_aifs
+import src.original.MJT_UoEdinburgh_UK.pk_models as edinburgh2_models
+import src.original.MJT_UoEdinburgh_UK.dce_fit as edinburgh2_fit
+import src.original.OGJ_OsloU_NOR.MRImageAnalysis.DCE.Analyze as oslo
+import src.original.ST_USydAUS.ModelDictionary as sydney
+from src.original.MB_QBI_UoManchester_UK.QbiPy.dce_models import dce_aif as manchester_aif
+from src.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):

src/wrappers/vfa.py

@@ -1,7 +1,7 @@
-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
+import src.original.MJT_UoEdinburgh_UK.t1_fit as edinburgh
+import src.original.ST_USydAUS.VFAT1mapping as sydney
+import src.original.McGill_CAN.vfa as mcgill
+src.utils.nb import percenterror
 import matplotlib.pyplot as plt
 import numpy as np
 

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_UoEdinburgh_UK.PharmacokineticModelling.models import ExtKety
+from src.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, ' \

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_UoManchester_UK.QbiPy.dce_models import tofts_model, dce_aif
+from src.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, ' \

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_UoEdinburgh_UK import dce_fit, pk_models, aifs
+from src.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, ' \

test/DCEmodels/test_DCEmodels_etofts_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_NOR.MRImageAnalysis.DCE.Analyze \
+from src.original.OGJ_OsloU_NOR.MRImageAnalysis.DCE.Analyze \
     import fitToModel
 
 # All tests will use the same arguments and same data...

test/DCEmodels/test_DCEmodels_etofts_OG_MO_AUMC_ICR_RMH_NL_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.OG_MO_AUMC_ICR_RMH_NL_UK.ExtendedTofts.DCE \
+from src.original.OG_MO_AUMC_ICR_RMH_NL_UK.ExtendedTofts.DCE \
     import \
     fit_tofts_model, fit_aif
 

test/DCEmodels/test_DCEmodels_etofts_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 osipi_code_collection.original.ST_USyd_AUS.ModelDictionary import ExtendedTofts
+from src.original.ST_USyd_AUS.ModelDictionary import ExtendedTofts
 
 # 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, ' \

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_USA.dce import fit_tofts
+from src.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 '

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_UoEdinburgh_UK.PharmacokineticModelling.models import ExtKety, Kety
+from src.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'

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_UoEdinburgh_UK import dce_fit, pk_models, aifs
+from src.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 '

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_NOR.MRImageAnalysis.DCE.Analyze import fitToModel
+from src.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, ' \

test/DCEmodels/test_DCEmodels_tofts_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 osipi_code_collection.original.ST_USyd_AUS.ModelDictionary import Tofts
+from src.original.ST_USyd_AUS.ModelDictionary import 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 '

test/PopulationAIF_DCE/test_popAIF_Georgiou_PvH_NKI_NL.py

@@ -3,7 +3,7 @@
 import numpy as np
 from time import perf_counter
 from ..helpers import osipi_parametrize, log_init, log_results
-from osipi_code_collection.original.PvH_NKI_NL.AIF.PopulationAIF import GeorgiouAIF
+from src.original.PvH_NKI_NL.AIF.PopulationAIF import GeorgiouAIF
 from . import popAIF_data
 
 

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_UoManchester_UK.QbiPy.dce_models.dce_aif as dce_aif
+import src.original.MB_QBI_UoManchester_UK.QbiPy.dce_models.dce_aif as dce_aif
 from . import popAIF_data
 
 

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_UoEdinburgh_UK.aifs as aifs
+import src.original.MJT_UoEdinburgh_UK.aifs as aifs
 from . import popAIF_data
 
 

test/PopulationAIF_DCE/test_popAIF_Parker_PvH_NKI_NL.py

@@ -3,7 +3,7 @@
 import numpy as np
 from time import perf_counter
 from ..helpers import osipi_parametrize, log_init, log_results
-from osipi_code_collection.original.PvH_NKI_NL.AIF.PopulationAIF import ParkerAIF
+from src.original.PvH_NKI_NL.AIF.PopulationAIF import ParkerAIF
 from . import popAIF_data
 
 

test/PopulationAIF_DCE/test_popAIF_Parker_ST_USyd_AUS.py

@@ -3,7 +3,7 @@
 import numpy as np
 from time import perf_counter
 from ..helpers import osipi_parametrize, log_init, log_results
-from osipi_code_collection.original.ST_USyd_AUS.InputFunctions import AIF, variableAIF, arr_shift
+from src.original.ST_USyd_AUS.InputFunctions import AIF, variableAIF, arr_shift
 from . import popAIF_data
 
 

test/PopulationAIF_DCE/test_popAIF_preclinical_ST_USyd_AUS.py

@@ -3,7 +3,7 @@
 import numpy as np
 from time import perf_counter
 from ..helpers import osipi_parametrize, log_init, log_results
-from osipi_code_collection.original.ST_USyd_AUS.InputFunctions import preclinicalAIF
+from src.original.ST_USyd_AUS.InputFunctions import preclinicalAIF
 from . import popAIF_data
 
 

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_USA.dce import signal_to_conc
+from src.original.LCB_BNI_USA.dce import signal_to_conc
 
 
 # All tests will use the same arguments and same data...

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_UoEdinburgh_UK.SignalToConcentration import SI2Conc
+from src.original.LEK_UoEdinburgh_UK.SignalToConcentration import SI2Conc
 
 
 # All tests will use the same arguments and same data...

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_UoManchester_UK.QbiPy.dce_models.tissue_concentration import signal_to_concentration
+from src.original.MB_QBI_UoManchester_UK.QbiPy.dce_models.tissue_concentration import signal_to_concentration
 
 
 

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_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
+from src.original.MJT_UoEdinburgh_UK.signal_models import SPGR
+from src.original.MJT_UoEdinburgh_UK.relaxivity import CRLinear
+from src.original.MJT_UoEdinburgh_UK.dce_fit import SigToEnh
+from src.original.MJT_UoEdinburgh_UK.dce_fit import EnhToConc, EnhToConcSPGR
 
 
 # All tests will use the same arguments and same data...

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_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
+from src.original.OG_MO_AUMC_ICR_RMH_NL_UK.ExtendedTofts.DCE import dce_to_r1eff
+from src.original.OG_MO_AUMC_ICR_RMH_NL_UK.ExtendedTofts.DCE import r1eff_to_conc
 
 
 

test/SI_to_Conc/test_SI2Conc_ST_USyd_AUS.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.ST_USyd_AUS.signals2conc import signals2conc
+from src.original.ST_USyd_AUS.signals2conc import signals2conc
 
 
 # All tests will use the same arguments and same data...

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_UoEdinburgh_UK.t1_fit import VFALinear, VFANonLinear, VFA2Points
+from src.original.MJT_UoEdinburgh_UK.t1_fit import VFALinear, VFANonLinear, VFA2Points
 
 
 # All tests will use the same arguments and same data...

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_NL_UK.ExtendedTofts.DCE import R1_two_fas, R1_VFA
+from src.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...

test/T1_mapping/test_t1_ST_USyd_AUS.py

@@ -4,7 +4,7 @@
 from time import perf_counter
 from ..helpers import osipi_parametrize, log_init, log_results # helper for running tests on multiple cases
 from . import t1_data # module for providing all t1 test cases
-from osipi_code_collection.original.ST_USyd_AUS.VFAT1mapping import VFAT1mapping # functions to test
+from src.original.ST_USyd_AUS.VFAT1mapping import VFAT1mapping # functions to test
 
 
 # All tests will use the same arguments and same data...

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.ZA_McGill_CAN.vfa import despot, novifast
+from src.original.ZA_McGill_CAN.vfa import despot, novifast
 
 
 # All tests will use the same arguments and same data...