added 5 MR tags: RepetitionTime, EchoTime, ScanSequence, MagneticFiel… (

#70) * added 5 MR tags: RepetitionTime, EchoTime, ScanSequence, MagneticFieldStrength, ImagedNucleus * added SEGMENTATION ReferencedSeriesSequence as ref_ct * change pytest version
bhklab · Feb 13, 2023 · 8f81e40 · 8f81e40
1 parent 1e25c57
commit 8f81e40
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Showing 2 changed files with 55 additions and 17 deletions.
diff --git a/.github/workflows/main-ci.yml b/.github/workflows/main-ci.yml
@@ -29,7 +29,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest setuptools wheel twine
+        python -m pip install flake8 pytest==7.2.0 setuptools wheel twine
         pip install -e .
         pip install -r requirements.txt
     - name: Import checking

diff --git a/imgtools/utils/crawl.py b/imgtools/utils/crawl.py
@@ -24,7 +24,8 @@ def crawl_one(folder):
                 series   = str(meta.SeriesInstanceUID)
                 instance = str(meta.SOPInstanceUID)
 
-                reference_ct, reference_rs, reference_pl = " ", " ", " "
+                reference_ct, reference_rs, reference_pl,  = "", "", ""
+                tr, te, tesla, scan_seq, elem = "", "", "", "", ""
                 try:
                     orientation = str(meta.ImageOrientationPatient) # (0020, 0037)
                 except:
@@ -38,19 +39,45 @@ def crawl_one(folder):
                 try: #RTSTRUCT
                     reference_ct = str(meta.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence[0].RTReferencedSeriesSequence[0].SeriesInstanceUID)
                 except: 
-                    try: #RTDOSE
-                        reference_rs = str(meta.ReferencedStructureSetSequence[0].ReferencedSOPInstanceUID)
+                    try: #SEGMENTATION
+                        reference_ct = str(meta.ReferencedSeriesSequence[0].SeriesInstanceUID)
                     except:
-                        pass
-                    try:
-                        reference_ct = str(meta.ReferencedImageSequence[0].ReferencedSOPInstanceUID)
-                    except:
-                        pass
-                    try:
-                        reference_pl = str(meta.ReferencedRTPlanSequence[0].ReferencedSOPInstanceUID)
-                    except:
-                        pass
+                        try: #RTDOSE
+                            reference_rs = str(meta.ReferencedStructureSetSequence[0].ReferencedSOPInstanceUID)
+                        except:
+                            pass
+                        try:
+                            reference_ct = str(meta.ReferencedImageSequence[0].ReferencedSOPInstanceUID)
+                        except:
+                            pass
+                        try:
+                            reference_pl = str(meta.ReferencedRTPlanSequence[0].ReferencedSOPInstanceUID)
+                        except:
+                            pass
 
+                #MRI Tags
+                try:
+                    tr = float(meta.RepetitionTime)
+                except:
+                    pass
+                try:
+                    te = float(meta.EchoTime)
+                except:
+                    pass
+                try:
+                    scan_seq = str(meta.ScanningSequence)
+                except:
+                    pass
+                try:
+                    tesla = float(meta.MagneticFieldStrength)
+                except:
+                    pass
+                try:
+                    elem = str(meta.ImagedNucleus)
+                except:
+                    pass
+
+
                 try:
                     reference_frame = str(meta.FrameOfReferenceUID)
                 except:
@@ -95,7 +122,13 @@ def crawl_one(folder):
                                                                    'reference_frame': reference_frame,
                                                                    'folder': rel_path,
                                                                    'orientation': orientation,
-                                                                   'orientation_type': orientation_type}
+                                                                   'orientation_type': orientation_type,
+                                                                   'repetition_time':tr,
+                                                                   'echo_time':te,
+                                                                   'scan_sequence': scan_seq,
+                                                                   'mag_field_strength': tesla,
+                                                                   'imaged_nucleus': elem
+                                                                   }
 
                 database[patient][study][series][subseries]['instances'].append(instance)
             except:
@@ -115,14 +148,19 @@ def to_df(database_dict):
                                        'series', 'series_description', 'subseries', 'modality', 
                                        'instances', 'instance_uid', 
                                        'reference_ct', 'reference_rs', 'reference_pl', 'reference_frame', 'folder',
-                                       'orientation', 'orientation_type']
+                                       'orientation', 'orientation_type', 'MR_repetition_time', 'MR_echo_time', 
+                                       'MR_scan_sequence', 'MR_magnetic_field_strength', 'MR_imaged_nucleus']
                             values = [pat, study, database_dict[pat][study]['description'], 
                                       series, database_dict[pat][study][series]['description'], 
                                       subseries, database_dict[pat][study][series][subseries]['modality'], 
-                                      len(database_dict[pat][study][series][subseries]['instances']), database_dict[pat][study][series][subseries]['instance_uid'], 
+                                      database_dict[pat][study][series][subseries]['instances'], database_dict[pat][study][series][subseries]['instance_uid'], 
                                       database_dict[pat][study][series][subseries]['reference_ct'], database_dict[pat][study][series][subseries]['reference_rs'], 
                                       database_dict[pat][study][series][subseries]['reference_pl'], database_dict[pat][study][series][subseries]['reference_frame'], database_dict[pat][study][series][subseries]['folder'],
-                                      database_dict[pat][study][series][subseries]['orientation'], database_dict[pat][study][series][subseries]['orientation_type']]
+                                      database_dict[pat][study][series][subseries]['orientation'], database_dict[pat][study][series][subseries]['orientation_type'],
+                                      database_dict[pat][study][series][subseries]['repetition_time'], database_dict[pat][study][series][subseries]['echo_time'],
+                                      database_dict[pat][study][series][subseries]['scan_sequence'], database_dict[pat][study][series][subseries]['mag_field_strength'], database_dict[pat][study][series][subseries]['imaged_nucleus'],
+                                      ]
+
                             df_add = pd.DataFrame([values], columns=columns)
                             df = pd.concat([df, df_add], ignore_index=True)
     return df