put metadata stuff into a util file

bhklab · Jun 8, 2022 · 69f4ee7 · 69f4ee7
1 parent 2ce5ade
commit 69f4ee7
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Showing 9 changed files with 324 additions and 200 deletions.
diff --git a/examples/autotest.py b/examples/autotest.py
@@ -243,7 +243,7 @@ def save_data(self):
         for col in self.output_df.columns:
             if col.startswith("folder"):
                 self.output_df[col] = self.output_df[col].apply(lambda x: pathlib.Path(x).as_posix().split(self.input_directory)[1][1:]) # rel path, exclude the slash at the beginning
-                folder_renames[col] = f"output_{col}"
+                folder_renames[col] = f"input_{col}"
         self.output_df.rename(columns=folder_renames, inplace=True)
         self.output_df.to_csv(self.output_df_path)
         shutil.rmtree(pathlib.Path(self.output_directory, ".temp").as_posix())

diff --git a/imgtools/io/loaders.py b/imgtools/io/loaders.py
@@ -16,8 +16,9 @@
 from ..modules import StructureSet
 from ..modules import Dose
 from ..modules import PET
-from ..modules import CTMRScan
+from ..modules import Scan
 from ..utils.crawl import *
+from ..utils.dicomutils import *
 
 
 
@@ -30,7 +31,7 @@ def read_header(path):
 def read_dicom_series(path: str,
                       series_id: Optional[str] = None,
                       recursive: bool = False,
-                      modality: str = "CT") -> CTMRScan:
+                      modality: str = "CT") -> Scan:
     """Read DICOM series as SimpleITK Image.
 
     Parameters
@@ -69,74 +70,74 @@ def read_dicom_series(path: str,
     reader.LoadPrivateTagsOn()
 
     metadata = {}
-    dicom_data = dcmread(dicom_names[0])
-    if modality == 'CT':
-        if hasattr(dicom_data, 'KVP'):
-            metadata["KVP"] = str(dicom_data.KVP)
-        if hasattr(dicom_data, 'XRayTubeCurrent'):
-            metadata["XRayTubeCurrent"] = str(dicom_data.XRayTubeCurrent)
-        if hasattr(dicom_data, 'ScanOptions'):
-            metadata["ScanOptions"] = str(dicom_data.ScanOptions)
-        if hasattr(dicom_data, 'ReconstructionAlgorithm'):
-            metadata["ReconstructionAlgorithm"] = str(dicom_data.ReconstructionAlgorithm)
-        if hasattr(dicom_data, 'ContrastFlowRate'):
-            metadata["ContrastFlowRate"] = str(dicom_data.ContrastFlowRate)
-        if hasattr(dicom_data, 'ContrastFlowDuration'):
-            metadata["ContrastFlowDuration"] = str(dicom_data.ContrastFlowDuration)
-        # is this contrast type?
-        if hasattr(dicom_data, 'ContrastBolusAgent'):
-            metadata["ContrastType"] = str(dicom_data.ContrastBolusAgent)
-    else: # MR
-        if hasattr(dicom_data, 'AcquisitionTime'):
-            metadata["AcquisitionTime"] = str(dicom_data.AcquisitionTime)
-        if hasattr(dicom_data, 'AcquisitionContrast'):
-            metadata["AcquisitionContrast"] = str(dicom_data.AcquisitionContrast)
-        if hasattr(dicom_data, 'AcquisitionType'):
-            metadata["AcquisitionType"] = str(dicom_data.AcquisitionType)
-        if hasattr(dicom_data, 'RepetitionTime'):
-            metadata["RepetitionTime"] = str(dicom_data.RepetitionTime)
-        if hasattr(dicom_data, 'EchoTime'):
-            metadata["EchoTime"] = str(dicom_data.EchoTime)
-        if hasattr(dicom_data, 'ImagingFrequency'):
-            metadata["ImagingFrequency"] = str(dicom_data.ImagingFrequency)
-        if hasattr(dicom_data, 'MagneticFieldStrength'):
-            metadata["MagneticFieldStrength"] = str(dicom_data.MagneticFieldStrength)
-
-    # Number of Slices is avg. number slice?
-    if hasattr(dicom_data, 'BodyPartExamined'):
-        metadata["BodyPartExamined"] = str(dicom_data.BodyPartExamined)
-    if hasattr(dicom_data, 'DataCollectionDiameter'):
-        metadata["DataCollectionDiameter"] = str(dicom_data.DataCollectionDiameter)
-    if hasattr(dicom_data, 'NumberofSlices'):
-        metadata["NumberofSlices"] = str(dicom_data.NumberofSlices)
-    # Slice Thickness is avg. slice thickness?
-    if hasattr(dicom_data, 'SliceThickness'):
-        metadata["SliceThickness"] = str(dicom_data.SliceThickness)
-    if hasattr(dicom_data, 'ScanType'):
-        metadata["ScanType"] = str(dicom_data.ScanType)
-    # Scan Progression Direction is Scan Direction?
-    if hasattr(dicom_data, 'ScanProgressionDirection'):
-        metadata["ScanProgressionDirection"] = str(dicom_data.ScanProgressionDirection)
-    if hasattr(dicom_data, 'PatientPosition'):
-        metadata["PatientPosition"] = str(dicom_data.PatientPosition)
-    # is this contrast type?
-    if hasattr(dicom_data, 'ContrastBolusAgent'):
-        metadata["ContrastType"] = str(dicom_data.ContrastBolusAgent)
-    if hasattr(dicom_data, 'Manufacturer'):
-        metadata["Manufacturer"] = str(dicom_data.Manufacturer)
-    # Scan Plane?
-    if hasattr(dicom_data, 'ScanOptions'):
-        metadata["ScanOptions"] = str(dicom_data.ScanOptions)
-    if hasattr(dicom_data, 'RescaleType'):
-        metadata["RescaleType"] = str(dicom_data.RescaleType)
-    if hasattr(dicom_data, 'RescaleSlope'):
-        metadata["RescaleSlope"] = str(dicom_data.RescaleSlope)
-    if hasattr(dicom_data, 'PixelSpacing') and hasattr(dicom_data, 'SliceThickness'):
-        pixel_size = copy.copy(dicom_data.PixelSpacing)
-        pixel_size.append(dicom_data.SliceThickness)
-        metadata["PixelSize"] = str(tuple(pixel_size))
-
-    return CTMRScan(reader.Execute(), metadata)
+    # dicom_data = dcmread(dicom_names[0])
+    # if modality == 'CT':
+    #     if hasattr(dicom_data, 'KVP'):
+    #         metadata["KVP"] = str(dicom_data.KVP)
+    #     if hasattr(dicom_data, 'XRayTubeCurrent'):
+    #         metadata["XRayTubeCurrent"] = str(dicom_data.XRayTubeCurrent)
+    #     if hasattr(dicom_data, 'ScanOptions'):
+    #         metadata["ScanOptions"] = str(dicom_data.ScanOptions)
+    #     if hasattr(dicom_data, 'ReconstructionAlgorithm'):
+    #         metadata["ReconstructionAlgorithm"] = str(dicom_data.ReconstructionAlgorithm)
+    #     if hasattr(dicom_data, 'ContrastFlowRate'):
+    #         metadata["ContrastFlowRate"] = str(dicom_data.ContrastFlowRate)
+    #     if hasattr(dicom_data, 'ContrastFlowDuration'):
+    #         metadata["ContrastFlowDuration"] = str(dicom_data.ContrastFlowDuration)
+    #     # is this contrast type?
+    #     if hasattr(dicom_data, 'ContrastBolusAgent'):
+    #         metadata["ContrastType"] = str(dicom_data.ContrastBolusAgent)
+    # else: # MR
+    #     if hasattr(dicom_data, 'AcquisitionTime'):
+    #         metadata["AcquisitionTime"] = str(dicom_data.AcquisitionTime)
+    #     if hasattr(dicom_data, 'AcquisitionContrast'):
+    #         metadata["AcquisitionContrast"] = str(dicom_data.AcquisitionContrast)
+    #     if hasattr(dicom_data, 'AcquisitionType'):
+    #         metadata["AcquisitionType"] = str(dicom_data.AcquisitionType)
+    #     if hasattr(dicom_data, 'RepetitionTime'):
+    #         metadata["RepetitionTime"] = str(dicom_data.RepetitionTime)
+    #     if hasattr(dicom_data, 'EchoTime'):
+    #         metadata["EchoTime"] = str(dicom_data.EchoTime)
+    #     if hasattr(dicom_data, 'ImagingFrequency'):
+    #         metadata["ImagingFrequency"] = str(dicom_data.ImagingFrequency)
+    #     if hasattr(dicom_data, 'MagneticFieldStrength'):
+    #         metadata["MagneticFieldStrength"] = str(dicom_data.MagneticFieldStrength)
+
+    # # Number of Slices is avg. number slice?
+    # if hasattr(dicom_data, 'BodyPartExamined'):
+    #     metadata["BodyPartExamined"] = str(dicom_data.BodyPartExamined)
+    # if hasattr(dicom_data, 'DataCollectionDiameter'):
+    #     metadata["DataCollectionDiameter"] = str(dicom_data.DataCollectionDiameter)
+    # if hasattr(dicom_data, 'NumberofSlices'):
+    #     metadata["NumberofSlices"] = str(dicom_data.NumberofSlices)
+    # # Slice Thickness is avg. slice thickness?
+    # if hasattr(dicom_data, 'SliceThickness'):
+    #     metadata["SliceThickness"] = str(dicom_data.SliceThickness)
+    # if hasattr(dicom_data, 'ScanType'):
+    #     metadata["ScanType"] = str(dicom_data.ScanType)
+    # # Scan Progression Direction is Scan Direction?
+    # if hasattr(dicom_data, 'ScanProgressionDirection'):
+    #     metadata["ScanProgressionDirection"] = str(dicom_data.ScanProgressionDirection)
+    # if hasattr(dicom_data, 'PatientPosition'):
+    #     metadata["PatientPosition"] = str(dicom_data.PatientPosition)
+    # # is this contrast type?
+    # if hasattr(dicom_data, 'ContrastBolusAgent'):
+    #     metadata["ContrastType"] = str(dicom_data.ContrastBolusAgent)
+    # if hasattr(dicom_data, 'Manufacturer'):
+    #     metadata["Manufacturer"] = str(dicom_data.Manufacturer)
+    # # Scan Plane?
+    # if hasattr(dicom_data, 'ScanOptions'):
+    #     metadata["ScanOptions"] = str(dicom_data.ScanOptions)
+    # if hasattr(dicom_data, 'RescaleType'):
+    #     metadata["RescaleType"] = str(dicom_data.RescaleType)
+    # if hasattr(dicom_data, 'RescaleSlope'):
+    #     metadata["RescaleSlope"] = str(dicom_data.RescaleSlope)
+    # if hasattr(dicom_data, 'PixelSpacing') and hasattr(dicom_data, 'SliceThickness'):
+    #     pixel_size = copy.copy(dicom_data.PixelSpacing)
+    #     pixel_size.append(dicom_data.SliceThickness)
+    #     metadata["PixelSize"] = str(tuple(pixel_size))
+
+    return Scan(reader.Execute(), metadata)
 
 
 def read_dicom_rtstruct(path):
@@ -155,14 +156,30 @@ def read_dicom_auto(path, series=None):
     dcms = glob.glob(pathlib.Path(path, "*.dcm").as_posix())
     meta = dcmread(dcms[0])
     modality = meta.Modality
+    all_modality_metadata = all_modalities_metadata(meta)
     if modality == 'CT' or modality == 'MR':
-        return read_dicom_series(path,series, modality=modality)
+        dicom_series = read_dicom_series(path,series, modality=modality)
+        if modality == 'CT':
+            dicom_series.metadata.update(ct_metadata(meta))
+            dicom_series.metadata.update(all_modality_metadata)
+        else:
+            dicom_series.metadata.update(mr_metadata(meta))
+            dicom_series.metadata.update(all_modality_metadata)
+        return dicom_series
     elif modality == 'PT':
-        return read_dicom_pet(path,series)
+        pet = read_dicom_pet(path,series)
+        pet.metadata.update(pet_metadata(meta))
+        pet.metadata.update(all_modality_metadata)
+        return pet
     elif modality == 'RTSTRUCT':
-        return read_dicom_rtstruct(dcms[0])
+        rtstruct = read_dicom_rtstruct(dcms[0])
+        rtstruct.metadata.update(rtstruct_metadata(meta))
+        rtstruct.metadata.update(all_modality_metadata)
+        return rtstruct
     elif modality == 'RTDOSE':
-        return read_dicom_rtdose(path)
+        rtdose = read_dicom_rtdose(path)
+        rtdose.metadata.update(all_modality_metadata)
+        return rtdose
     else:
         if len(dcms)==1:
             raise NotImplementedError

diff --git a/imgtools/modules/__init__.py b/imgtools/modules/__init__.py
@@ -4,4 +4,4 @@
 from .dose import *
 from .datagraph import *
 from .sparsemask import *
-from .ctmrscan import *
+from .scan import *
diff --git a/imgtools/modules/dose.py b/imgtools/modules/dose.py
@@ -29,6 +29,8 @@ def __init__(self, img_dose, df, metadata: Optional[Dict[str, T]] = None):
         self.df = df
         if metadata:
             self.metadata = metadata
+        else:
+            self.metadata = {}
 
     @classmethod
     def from_dicom_rtdose(cls, path):
@@ -50,44 +52,44 @@ def from_dicom_rtdose(cls, path):
         metadata = {}
         # metadata["DoseType"] = df.DoseType
         #return cls(img_dose, df, metadata)
-        if hasattr(df, 'BodyPartExamined'):
-            metadata["BodyPartExamined"] = str(df.BodyPartExamined)
-        if hasattr(df, 'DataCollectionDiameter'):
-            metadata["DataCollectionDiameter"] = str(df.DataCollectionDiameter)
-        # Number of Slices is avg. number slice?
-        if hasattr(df, 'NumberofSlices'):
-            metadata["NumberofSlices"] = str(df.NumberofSlices)
-        # Slice Thickness is avg. slice thickness?
-        if hasattr(df, 'SliceThickness'):
-            metadata["SliceThickness"] = str(df.SliceThickness)
-        if hasattr(df, 'ScanType'):
-            metadata["ScanType"] = str(df.ScanType)
-        # Scan Progression Direction is Scan Direction?
-        if hasattr(df, 'ScanProgressionDirection'):
-            metadata["ScanProgressionDirection"] = str(df.ScanProgressionDirection)
-        if hasattr(df, 'PatientPosition'):
-            metadata["PatientPosition"] = str(df.PatientPosition)
-        # is this contrast type?
-        if hasattr(df, 'ContrastBolusAgent'):
-            metadata["ContrastType"] = str(df.ContrastBolusAgent)
-        if hasattr(df, 'Manufacturer'):
-            metadata["Manufacturer"] = str(df.Manufacturer)
-        # Which field of view?
-        # if hasattr(df, 'FieldOfViewDescription'):
-        #     metadata["FieldOfViewDescription"] = str(df.FieldOfViewDescription)
-        # Scan Plane?
-        if hasattr(df, 'ScanOptions'):
-            metadata["ScanOptions"] = str(df.ScanOptions)
-        if hasattr(df, 'RescaleType'):
-            metadata["RescaleType"] = str(df.RescaleType)
-        if hasattr(df, 'RescaleSlope'):
-            metadata["RescaleSlope"] = str(df.RescaleSlope)
-        if hasattr(df, 'PixelSpacing') and hasattr(df, 'SliceThickness'):
-            pixel_size = copy.copy(df.PixelSpacing)
-            pixel_size.append(df.SliceThickness)
-            metadata["PixelSize"] = str(tuple(pixel_size))
-
-        return cls(img_dose, df)
+        # if hasattr(df, 'BodyPartExamined'):
+        #     metadata["BodyPartExamined"] = str(df.BodyPartExamined)
+        # if hasattr(df, 'DataCollectionDiameter'):
+        #     metadata["DataCollectionDiameter"] = str(df.DataCollectionDiameter)
+        # # Number of Slices is avg. number slice?
+        # if hasattr(df, 'NumberofSlices'):
+        #     metadata["NumberofSlices"] = str(df.NumberofSlices)
+        # # Slice Thickness is avg. slice thickness?
+        # if hasattr(df, 'SliceThickness'):
+        #     metadata["SliceThickness"] = str(df.SliceThickness)
+        # if hasattr(df, 'ScanType'):
+        #     metadata["ScanType"] = str(df.ScanType)
+        # # Scan Progression Direction is Scan Direction?
+        # if hasattr(df, 'ScanProgressionDirection'):
+        #     metadata["ScanProgressionDirection"] = str(df.ScanProgressionDirection)
+        # if hasattr(df, 'PatientPosition'):
+        #     metadata["PatientPosition"] = str(df.PatientPosition)
+        # # is this contrast type?
+        # if hasattr(df, 'ContrastBolusAgent'):
+        #     metadata["ContrastType"] = str(df.ContrastBolusAgent)
+        # if hasattr(df, 'Manufacturer'):
+        #     metadata["Manufacturer"] = str(df.Manufacturer)
+        # # Which field of view?
+        # # if hasattr(df, 'FieldOfViewDescription'):
+        # #     metadata["FieldOfViewDescription"] = str(df.FieldOfViewDescription)
+        # # Scan Plane?
+        # if hasattr(df, 'ScanOptions'):
+        #     metadata["ScanOptions"] = str(df.ScanOptions)
+        # if hasattr(df, 'RescaleType'):
+        #     metadata["RescaleType"] = str(df.RescaleType)
+        # if hasattr(df, 'RescaleSlope'):
+        #     metadata["RescaleSlope"] = str(df.RescaleSlope)
+        # if hasattr(df, 'PixelSpacing') and hasattr(df, 'SliceThickness'):
+        #     pixel_size = copy.copy(df.PixelSpacing)
+        #     pixel_size.append(df.SliceThickness)
+        #     metadata["PixelSize"] = str(tuple(pixel_size))
+
+        return cls(img_dose, df, metadata)
 
     def resample_dose(self,
                       ct_scan: sitk.Image) -> sitk.Image: