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Fix build system: Modernize dependencies and fix import paths (2300+ tests passing) #138

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Fix build system: Modernize dependencies and fix import paths (2300+ tests passing) #138

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7b9be87
Final fix: Corrected import syntax in test files
Aarshpatel12 Jan 21, 2026
7bec1c3
Fix: Update wrapper imports to use 'src' (Addresses review by @ltorres6)
Aarshpatel12 Jan 23, 2026
d97c31d
Fix: Add pydicom to dependencies
Aarshpatel12 Feb 2, 2026
9605229
Remove fixed version for dicom dependency
Aarshpatel12 Feb 2, 2026
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2 changes: 1 addition & 1 deletion MANIFEST.in
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include src/original/PvH_NKI_NL/AIF/PopulationAIF_GeorgiouMRM2018.txt
include from src.original/PvH_NKI_NL/AIF/PopulationAIF_GeorgiouMRM2018.txt
174 changes: 87 additions & 87 deletions doc/code_contributions_record.csv
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4 changes: 2 additions & 2 deletions notebooks/old_nb/DCE_ToftsModel.ipynb
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4 changes: 2 additions & 2 deletions notebooks/old_nb/T1mapping_QIBAv1.ipynb
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4 changes: 2 additions & 2 deletions notebooks/old_nb/T1mapping_QIBAv2.ipynb
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2 changes: 1 addition & 1 deletion setup.py
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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',
'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'],
include_package_data=True,
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3 changes: 2 additions & 1 deletion src/original/OGJ_OsloU_NOR/MRImageAnalysis/io.py
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import dicom, dicom.UID
import pydicom as dicom
import pydicom.uid
from dicom.dataset import Dataset, FileDataset
import datetime, time
import os
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6 changes: 3 additions & 3 deletions src/wrappers/tofts.py
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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
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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
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):
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2 changes: 1 addition & 1 deletion src/wrappers/vfa.py
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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
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from osipi_code_collection.utils.nb import percenterror
src.utils.nb import percenterror
import matplotlib.pyplot as plt
import numpy as np

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2 changes: 1 addition & 1 deletion test/DCEmodels/test_DCEmodels_etofts_LEK_UoEdinburgh_UK.py
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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, ' \
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2 changes: 1 addition & 1 deletion test/DCEmodels/test_DCEmodels_etofts_MB_QBI_UoManchester_UK.py
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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, ' \
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2 changes: 1 addition & 1 deletion test/DCEmodels/test_DCEmodels_etofts_MJT_UoEdinburgh_UK.py
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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, ' \
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2 changes: 1 addition & 1 deletion test/DCEmodels/test_DCEmodels_etofts_OGJ_OsloU_NOR.py
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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...
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2 changes: 1 addition & 1 deletion test/DCEmodels/test_DCEmodels_etofts_OG_MO_AUMC_ICR_RMH_NL_UK.py
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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

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2 changes: 1 addition & 1 deletion test/DCEmodels/test_DCEmodels_etofts_ST_USyd_AUS.py
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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, ' \
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2 changes: 1 addition & 1 deletion test/DCEmodels/test_DCEmodels_tofts_LCB_BNI_USA.py
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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 '
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2 changes: 1 addition & 1 deletion test/DCEmodels/test_DCEmodels_tofts_LEK_UoEdinburgh_UK.py
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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'
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2 changes: 1 addition & 1 deletion test/DCEmodels/test_DCEmodels_tofts_MJT_UoEdinburgh_UK.py
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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 '
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2 changes: 1 addition & 1 deletion test/DCEmodels/test_DCEmodels_tofts_OGJ_OsloU_NOR.py
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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, ' \
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2 changes: 1 addition & 1 deletion test/DCEmodels/test_DCEmodels_tofts_ST_USyd_AUS.py
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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 '
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2 changes: 1 addition & 1 deletion test/PopulationAIF_DCE/test_popAIF_Georgiou_PvH_NKI_NL.py
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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


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2 changes: 1 addition & 1 deletion test/PopulationAIF_DCE/test_popAIF_Parker_MB_QBI_UoManchester_UK.py
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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


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2 changes: 1 addition & 1 deletion test/PopulationAIF_DCE/test_popAIF_Parker_MJT_Edinburgh_UK.py
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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


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2 changes: 1 addition & 1 deletion test/PopulationAIF_DCE/test_popAIF_Parker_PvH_NKI_NL.py
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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


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2 changes: 1 addition & 1 deletion test/PopulationAIF_DCE/test_popAIF_Parker_ST_USyd_AUS.py
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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


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2 changes: 1 addition & 1 deletion test/PopulationAIF_DCE/test_popAIF_preclinical_ST_USyd_AUS.py
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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


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2 changes: 1 addition & 1 deletion test/SI_to_Conc/test_SI2Conc_LCB_BNI_USA.py
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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...
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2 changes: 1 addition & 1 deletion test/SI_to_Conc/test_SI2Conc_LEK_Edinburgh_UK.py
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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...
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2 changes: 1 addition & 1 deletion test/SI_to_Conc/test_SI2Conc_MB_QBI_UoManchester_UK.py
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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



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8 changes: 4 additions & 4 deletions test/SI_to_Conc/test_SI2Conc_MJT_UoEdinburgh_UK.py
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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...
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4 changes: 2 additions & 2 deletions test/SI_to_Conc/test_SI2Conc_OG_MO_AUMC_ICR_RMH_NL_UK.py
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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



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2 changes: 1 addition & 1 deletion test/SI_to_Conc/test_SI2Conc_ST_USyd_AUS.py
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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...
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2 changes: 1 addition & 1 deletion test/T1_mapping/test_t1_MJT_Edinburgh_UK.py
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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...
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2 changes: 1 addition & 1 deletion test/T1_mapping/test_t1_OG_MO_AUMC_ICR_RMH_NL_UK.py
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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...
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2 changes: 1 addition & 1 deletion test/T1_mapping/test_t1_ST_USyd_AUS.py
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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...
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2 changes: 1 addition & 1 deletion test/T1_mapping/test_t1_ZA_McGill_CAN.py
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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...
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