minor changes

BIMCV-CSUSP · Aug 24, 2023 · 2239af8 · 2239af8
1 parent fdbaf7c
commit 2239af8
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Showing 4 changed files with 17 additions and 15 deletions.
diff --git a/xnat2mids/__main__.py b/xnat2mids/__main__.py
@@ -161,13 +161,13 @@ def main():
         print(f"{xnat_data_path}")
         print(f"{mids_data_path}")
 
-        # print("MIDS are generating...")
-        # create_directory_mids_v1(
-        #     xnat_data_path,
-        #     mids_data_path,
-        #     body_part,
-        #     debug_level
-        # )
+        print("MIDS are generating...")
+        create_directory_mids_v1(
+            xnat_data_path,
+            mids_data_path,
+            body_part,
+            debug_level
+        )
 
         print("participats tsv are generating...")
         create_tsvs(xnat_data_path, mids_data_path, body_part)

diff --git a/xnat2mids/mids_conversion.py b/xnat2mids/mids_conversion.py
@@ -13,11 +13,11 @@
 from xnat2mids.conversion.dicom_converters import dicom2niix
 from xnat2mids.conversion.dicom_converters import dicom2png
 from tqdm import tqdm
-
+from pandas.errors import EmptyDataError
 
 adquisition_date_pattern = r"(?P<year>\d+)-(?P<month>\d+)-(?P<day>\d+)T(?P<hour>\d+):(?P<minutes>\d+):(?P<seconds>\d+).(?P<ms>\d+)"
 subses_pattern = r"[A-z]+(?P<prefix_sub>\d*)?(_S)(?P<suffix_sub>\d+)/[A-z]+\-?[A-z]*(?P<prefix_ses>\d*)?(_E)(?P<suffix_ses>\d+)"
-prostate_pattern = r"(?:(?:(?:diff?|dwi)(?:\W|_)(?:.*)(?:b\d+))|dif 2000)|(?:adc|Apparent)|prop|blade|fse|tse"
+prostate_pattern = r"(?:(?:(?:diff?|dwi)(?:\W|_)(?:.*)(?:b\d+))|dif 2000)|(?:adc|Apparent)|prop|blade|fse|tse|^ax T2$"
 
 aquisition_date_pattern_comp = re.compile(adquisition_date_pattern)
 prostate_pattern_comp = re.compile(prostate_pattern, re.I)
@@ -188,10 +188,11 @@ def create_directory_mids_v1(xnat_data_path, mids_data_path, body_part, debug_le
                             json_adquisitions = {
                                 f'{k}': dict_json.get(k, -1) for k in dict_mr_keys.keys()
                             }
-
-                            protocol, acq, task, ce, rec, dir_, part, folder_BIDS = tagger.classification_by_min_max(json_adquisitions)
-                            print(protocol, acq, task, ce, rec, dir_, part, folder_BIDS)
-
+                            try:
+                                protocol, acq, task, ce, rec, dir_, part, folder_BIDS = tagger.classification_by_min_max(json_adquisitions)
+                                print(protocol, acq, task, ce, rec, dir_, part, folder_BIDS)
+                            except EmptyDataError as e:
+                                continue
                             procedure_class_mr.control_sequences(
                                 folder_conversion, mids_session_path, session_name, protocol, acq, dir_, folder_BIDS, body_part
                             )

diff --git a/xnat2mids/protocols/protocol_RM_prostate.tsv b/xnat2mids/protocols/protocol_RM_prostate.tsv
@@ -1,7 +1,7 @@
 	Protocol	acq	task	rec	ce	dir	part	folder	Manufacturer	ManufacturersModelName	ScanningSequence	SequenceVariant	ScanOptions	SequenceName	ImageType	AngioFlag	MagneticFieldStrength	RepetitionTime	InversionTime	FlipAngle	EchoTime	NumberOfAverages	RawImage	DerivedVendorReportedEchoSpacing	EffectiveEchoSpacing	TotalReadoutTime
 	T2w	propeller						anat	"[""GE""]"	"[""SIGNA Architect"", ""Optima MR450w""]"	"[""RM"", ""SE""]"	"[""OSP"", ""SK""]"	"[""FAST_GEMS\\PROP_GEMS\\NPW\\ACC_GEMS\\TRF_GEMS\\FSS_GEMS\\FILTERED_GEMS"", ""FAST_GEMS\\PROP_GEMS\\NPW\\ACC_GEMS\\TRF_GEMS\\FSS_GEMS"", ""FAST_GEMS\\PROP_GEMS\\NPW\\ACC_GEMS\\TRF_GEMS\\FILTERED_GEMS\\FSI_GEMS"", ""FAST_GEMS\\PROP_GEMS\\NPW\\ACC_GEMS\\TRF_GEMS\\FILTERED_GEMS\\FSL_GEMS"", ""FAST_GEMS\\PROP_GEMS\\NPW\\ACC_GEMS\\TRF_GEMS\\FSL_GEMS"", ""SAT_GEMS\\NPW\\NP\\EDR_GEMS\\TRF_GEMS\\ACC_GEMS\\SP\\FSL_GEMS\\FR_GEMS"", ""FAST_GEMS\\PROP_GEMS\\NPW\\ACC_GEMS\\SAT_GEMS\\FS\\TRF_GEMS\\FILTERED_GE"", ""FAST_GEMS\\PROP_GEMS\\NPW\\ACC_GEMS\\TRF_GEMS\\FILTERED_GEMS\\FSS_GEMS"", ""SAT_GEMS\\NPW\\NP\\EDR_GEMS\\TRF_GEMS\\FILTERED_GEMS\\ACC_GEMS\\SP\\FSL_G"", ""FAST_GEMS\\PROP_GEMS\\NPW\\ACC_GEMS\\TRF_GEMS\\FILTERED_GEMS""]"	[-1]	"[[""DERIVED"", ""PRIMARY"", ""PROPELLER"", ""NONE""], [""ORIGINAL"", ""PRIMARY"", ""OTHER""], [""ORIGINAL"", ""PRIMARY"", ""PROPELLER"", ""NONE""]]"	N	[1.5, 3.0]	[5.05891, 12.1146]	[-1]	[160.0, 160.0]	[0.08688, 0.158752]	[2.0, 3.0]	[-1]	[-1]	[-1]	[-1]
 	T2w	blade						anat	"[""Siemens""]"	"[""MAGNETOM Vida""]"	"[""SE""]"	"[""SP\\SK""]"	"[""SP\\PER"", ""PER"", ""SP\\CG\\RG\\PER"", ""CG\\RG\\PER""]"	"[""*tseB2d1_25"", ""*tseB2d1_40""]"	"[[""ORIGINAL"", ""PRIMARY"", ""M"", ""NORM"", ""DIS2D"", ""MFSPLIT""]]"	N	[3.0, 3.0]	[4.35, 12.75]	[-1]	[91.0, 160.0]	[0.113, 0.167]	[-1]	[-1]	[-1]	[-1]	[-1]
-	T2w	fse						anat	"[""GE""]"	"[""Signa HDxt"", ""SIGNA Architect"", ""Optima MR450w""]"	"[""SE"", ""IR""]"	"[""SK\\OSP"", ""SK""]"	"[""FAST_GEMS\\SAT_GEMS\\MP_GEMS\\FILTERED_GEMS\\ACC_GEMS\\PFP\\FS"", ""FAST_GEMS\\FC_FREQ_AX_GEMS\\FC\\EDR_GEMS\\SEQ_GEMS\\TRF_GEMS\\ACC_GEMS"", ""FAST_GEMS\\SAT_GEMS\\TRF_GEMS\\FILTERED_GEMS\\ACC_GEMS\\SP"", ""FAST_GEMS\\FC_FREQ_AX_GEMS\\FC\\EDR_GEMS\\SEQ_GEMS\\TRF_GEMS\\FILTERE"",""FAST_GEMS\\TRF_GEMS\\FILTERED_GEMS\\ACC_GEMS"", ""FAST_GEMS\\TRF_GEMS\\FILTERED_GEMS"", ""FAST_GEMS\\EDR_GEMS\\SS_GEMS\\FILTERED_GEMS\\ACC_GEMS\\PFP"", ""FAST_GEMS\\NPW\\NP\\EDR_GEMS\\TRF_GEMS\\FILTERED_GEMS\\ACC_GEMS\\FSL_GEM"", ""FAST_GEMS\\VB_GEMS\\SS_GEMS\\PFP"", ""FAST_GEMS\\VB_GEMS\\SS_GEMS\\FILTERED_GEMS\\PFP"", ""FAST_GEMS\\SAT_GEMS\\NPW\\NP\\EDR_GEMS\\TRF_GEMS\\FILTERED_GEMS\\SP\\FS"", ""FAST_GEMS\\NPW\\EDR_GEMS\\TRF_GEMS\\FILTERED_GEMS\\FSA_GEMS"", ""FAST_GEMS\\NPW\\EDR_GEMS\\TRF_GEMS\\FILTERED_GEMS\\FSI_GEMS"", ""FAST_GEMS\\FC_FREQ_AX_GEMS\\FC\\EDR_GEMS\\TRF_GEMS\\FILTERED_GEMS"", ""FAST_GEMS\\SAT_GEMS\\NPW\\EDR_GEMS\\TRF_GEMS\\FILTERED_GEMS\\SP\\FSP_GEM"", ""FAST_GEMS\\FC_FREQ_AX_GEMS\\FC\\NPW\\EDR_GEMS\\TRF_GEMS"", ""FAST_GEMS\\FC_SLICE_AX_GEMS\\FC\\NPW\\EDR_GEMS\\TRF_GEMS\\FILTERED_GEMS"", ""FAST_GEMS\\SS_GEMS\\FILTERED_GEMS\\ACC_GEMS\\PFP"", ""FAST_GEMS\\FC_FREQ_AX_GEMS\\FC\\SAT_GEMS\\NPW\\EDR_GEMS\\TRF_GEMS\\FILTE"", ""FAST_GEMS\\NPW\\NP\\EDR_GEMS\\TRF_GEMS\\FILTERED_GEMS\\FSI_GEMS"", ""FAST_GEMS\\SS_GEMS\\FILTERED_GEMS\\PFP"", ""FAST_GEMS\\FC_FREQ_AX_GEMS\\FC\\NPW\\EDR_GEMS\\TRF_GEMS\\FILTERED_GEMS""]"	[-1]	"[[""ORIGINAL"", ""PRIMARY"", ""OTHER""]]"	N	[1.5, 3.0]	[0.38, 8.98]	[-1]	[90.0, 180.0]	[0.086108, 0.12624]	[1.5, 2.0]	[-1]	[-1]	[-1]	[-1]
+	T2w	fse						anat	"[""GE""]"	"[""Signa HDxt"", ""SIGNA Architect"", ""Optima MR450w""]"	"[""SE"", ""IR""]"	"[""SK\\OSP"", ""SK""]"	"[""FAST_GEMS\\FC_SLICE_AX_GEMS\\FC\\SAT_GEMS\\NPW\\EDR_GEMS\\TRF_GEMS\\FILT"", ""FAST_GEMS\\SAT_GEMS\\MP_GEMS\\FILTERED_GEMS\\ACC_GEMS\\PFP\\FS"", ""FAST_GEMS\\FC_FREQ_AX_GEMS\\FC\\EDR_GEMS\\SEQ_GEMS\\TRF_GEMS\\ACC_GEMS"", ""FAST_GEMS\\SAT_GEMS\\TRF_GEMS\\FILTERED_GEMS\\ACC_GEMS\\SP"", ""FAST_GEMS\\FC_FREQ_AX_GEMS\\FC\\EDR_GEMS\\SEQ_GEMS\\TRF_GEMS\\FILTERE"",""FAST_GEMS\\TRF_GEMS\\FILTERED_GEMS\\ACC_GEMS"", ""FAST_GEMS\\TRF_GEMS\\FILTERED_GEMS"", ""FAST_GEMS\\EDR_GEMS\\SS_GEMS\\FILTERED_GEMS\\ACC_GEMS\\PFP"", ""FAST_GEMS\\NPW\\NP\\EDR_GEMS\\TRF_GEMS\\FILTERED_GEMS\\ACC_GEMS\\FSL_GEM"", ""FAST_GEMS\\VB_GEMS\\SS_GEMS\\PFP"", ""FAST_GEMS\\VB_GEMS\\SS_GEMS\\FILTERED_GEMS\\PFP"", ""FAST_GEMS\\SAT_GEMS\\NPW\\NP\\EDR_GEMS\\TRF_GEMS\\FILTERED_GEMS\\SP\\FS"", ""FAST_GEMS\\NPW\\EDR_GEMS\\TRF_GEMS\\FILTERED_GEMS\\FSA_GEMS"", ""FAST_GEMS\\NPW\\EDR_GEMS\\TRF_GEMS\\FILTERED_GEMS\\FSI_GEMS"", ""FAST_GEMS\\FC_FREQ_AX_GEMS\\FC\\EDR_GEMS\\TRF_GEMS\\FILTERED_GEMS"", ""FAST_GEMS\\SAT_GEMS\\NPW\\EDR_GEMS\\TRF_GEMS\\FILTERED_GEMS\\SP\\FSP_GEM"", ""FAST_GEMS\\FC_FREQ_AX_GEMS\\FC\\NPW\\EDR_GEMS\\TRF_GEMS"", ""FAST_GEMS\\FC_SLICE_AX_GEMS\\FC\\NPW\\EDR_GEMS\\TRF_GEMS\\FILTERED_GEMS"", ""FAST_GEMS\\SS_GEMS\\FILTERED_GEMS\\ACC_GEMS\\PFP"", ""FAST_GEMS\\FC_FREQ_AX_GEMS\\FC\\SAT_GEMS\\NPW\\EDR_GEMS\\TRF_GEMS\\FILTE"", ""FAST_GEMS\\NPW\\NP\\EDR_GEMS\\TRF_GEMS\\FILTERED_GEMS\\FSI_GEMS"", ""FAST_GEMS\\SS_GEMS\\FILTERED_GEMS\\PFP"", ""FAST_GEMS\\FC_FREQ_AX_GEMS\\FC\\NPW\\EDR_GEMS\\TRF_GEMS\\FILTERED_GEMS""]"	[-1]	"[[""ORIGINAL"", ""PRIMARY"", ""OTHER""]]"	N	[1.5, 3.0]	[0.38, 8.98]	[-1]	[90.0, 180.0]	[0.086108, 0.12624]	[1.5, 2.0]	[-1]	[-1]	[-1]	[-1]
 	T2w	fse						anat	"[""Siemens""]"	"[""MAGNETOM Vida""]"	"[""SE""]"	"[""SP\\SK""]"	"[""PER"", ""PFP\\CG\\RG\\PER"", ""SP\\CG\\RG\\PER"", ""CG\\RG\\PER""]"	"[""*tse2d1_25"", ""*tseB2d1_25"", ""*tir2d1_7""]"	"[[""ORIGINAL"", ""PRIMARY"", ""M"", ""NORM"", ""DIS2D"", ""MFSPLIT""], [""ORIGINAL"", ""PRIMARY"", ""M"", ""DIS2D"", ""NORM"", ""MFSPLIT""]]"	N	[3.0, 3.0]	[4.16, 11.19]	[-1]	[117.0, 160.0]	[0.038, 0.129]	[2.0, 4.0]	[-1]	[-1]	[-1]	[-1]
 	T2w	fse						anat	"[""Philips""]"	"[""Ingenia CX"", ""MR 5300""]"	"[""SE""]"	"[""SK""]"	"[""SP"", ""OTHER""]"	[-1]	"[[""ORIGINAL"", ""PRIMARY"", ""M"", ""SE"", ""M"", ""SE""]]"	N	[1.5, 1.5]	[6.0, 9.14193]	[-1]	[90.0, 90.0]	[0.12, 0.12]	[2.0, 2.0]	[-1]	[-1]	[-1]	[-1]
 	stir	fse						anat	"[""GE""]"	"[""Signa Hdxt""]"	"[""RM""]"	"[""OSP"", ""NONE""]"	"[""FC_FREQ_AX_GEMS\\FC\\SAT_GEMS\\EDR_GEMS\\SEQ_GEMS\\TRF_GEMS\\FILTERED_G"", ""FC_FREQ_AX_GEMS\\FC\\EDR_GEMS\\SEQ_GEMS\\TRF_GEMS\\FILTERED_GEMS\\ACC_G"", ""FC_FREQ_AX_GEMS\\FC\\NPW\\EDR_GEMS\\SEQ_GEMS\\TRF_GEMS"", ""FC_SLICE_AX_GEMS\\FC\\EDR_GEMS\\SEQ_GEMS\\TRF_GEMS\\ACC_GEMS"", ""FC_FREQ_AX_GEMS\\FC\\EDR_GEMS\\SEQ_GEMS\\TRF_GEMS"", ""FC_FREQ_AX_GEMS\\FC\\EDR_GEMS\\SEQ_GEMS\\TRF_GEMS\\ACC_GEMS""]"	[-1]	"[[""ORIGINAL"", ""PRIMARY"", ""OTHER""]]"	N	[3.0, 3.0]	[3.32, 6.24]	[0.18, 0.18]	[90.0, 90.0]	[0.0328, 0.054288]	[2.0, 2.0]	[-1]	[-1]	[-1]	[-1]

diff --git a/xnat2mids/protocols/scans_tagger.py b/xnat2mids/protocols/scans_tagger.py
@@ -2,7 +2,7 @@
 import numpy as np
 import json
 pd.set_option('display.max_columns', None)
-
+from pandas.errors import EmptyDataError
 class Tagger:
     # scan group
     #               SE = Spin Echo          =====>>>> 'SE'
@@ -45,6 +45,7 @@ def classification_by_min_max(self, dict_atrubutes):
         print("#" * 40, "table_protocol_M", "#" * 40)
         print(table_protocol_M[["Protocol", "acq"]])
 
+        if table_protocol_M.empty: raise EmptyDataError 
 
         table_protocol_M_SS = table_protocol_M[[
             any([True for s in json.loads(l) if s == scaning_sequence])