naming

Author: mjt320

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,

notebooks/contributors.ipynb

@@ -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

src/wrappers/tofts.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

src/wrappers/vfa.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, ' \

test/DCEmodels/test_DCEmodels_tofts_OGJ_OsloU_NOR.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

test/DSCmodels/test_DSCmodels_LcurveReg_SR_TBG_BNIPhoenixUSA.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...

test/T1_mapping/test_t1_ZA_McGill_CAN.py

@@ -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",