added modalities, num rtstruct and pixel size to metadata

examples/autotest.py

@@ -96,9 +96,11 @@ def process_one_subject(self, subject_id):
         print(subject_id, " start")
 
         metadata = {}
+        subject_modalities = set()
+        num_rtstructs = 0
         for i, colname in enumerate(self.output_streams):
             modality = colname.split("_")[0]
-
+            subject_modalities.add(modality)
             # Taking modality pairs if it exists till _{num}
             output_stream = ("_").join([item for item in colname.split("_") if item.isnumeric()==False])
 
@@ -154,6 +156,7 @@ def process_one_subject(self, subject_id):
 
                 print(subject_id, " SAVED DOSE")
             elif modality == "RTSTRUCT":
+                num_rtstructs += 1
                 #For RTSTRUCT, you need image or PT
                 structure_set = read_results[i]
                 conn_to = output_stream.split("_")[-1]
@@ -220,6 +223,8 @@ def process_one_subject(self, subject_id):
 
                 print(subject_id, " SAVED PET")
         #Saving all the metadata in multiple text files
+        metadata["Modalities"] = list(subject_modalities)
+        metadata["numRTSTRUCTs"] = num_rtstructs
         with open(pathlib.Path(self.output_directory,".temp",f'{subject_id}.pkl').as_posix(),'wb') as f:
             pickle.dump(metadata,f)
         return 

imgtools/io/loaders.py

@@ -3,7 +3,7 @@
 import re
 from typing import Optional, List
 from collections import namedtuple
-import json
+import copy
 
 import pandas as pd
 import SimpleITK as sitk
@@ -128,6 +128,10 @@ def read_dicom_series(path: str,
         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"] = tuple(pixel_size)
 
     return CTMRScan(reader.Execute(), metadata)
 

imgtools/modules/dose.py

@@ -1,5 +1,6 @@
 import os, pathlib
 import warnings
+import copy
 
 from typing import Dict, Optional, TypeVar
 
@@ -77,6 +78,10 @@ def from_dicom_rtdose(cls, path):
             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"] = tuple(pixel_size)
 
         return cls(img_dose, df)
 

imgtools/modules/pet.py

@@ -6,6 +6,7 @@
 from matplotlib import pyplot as plt
 import SimpleITK as sitk
 from pydicom import dcmread
+import copy
 
 T = TypeVar('T')
 
@@ -100,6 +101,10 @@ def from_dicom_pet(cls, path,series_id=None,type="SUV"):
             metadata["RescaleType"] = str(pet.RescaleType)
         if hasattr(pet, 'RescaleSlope'):
             metadata["RescaleSlope"] = str(pet.RescaleSlope)
+        if hasattr(pet, 'PixelSpacing') and hasattr(pet, 'SliceThickness'):
+            pixel_size = copy.copy(pet.PixelSpacing)
+            pixel_size.append(pet.SliceThickness)
+            metadata["PixelSize"] = tuple(pixel_size)
 
         return cls(img_pet, df, factor, calc, metadata)
         # return cls(img_pet, df, factor, calc)

imgtools/modules/structureset.py

@@ -1,6 +1,7 @@
 import re
 from warnings import warn
 from typing import Dict, List, Optional, Union, Tuple, Set, TypeVar
+import copy
 
 import numpy as np
 import SimpleITK as sitk
@@ -36,7 +37,7 @@ def from_dicom_rtstruct(cls, rtstruct_path: str) -> 'StructureSet':
 
         metadata = {}
         if hasattr(rtstruct, 'StructureSetROISequence'):
-            metadata["num_ROIs"] = str(len(rtstruct.StructureSetROISequence))
+            metadata["numROIs"] = str(len(rtstruct.StructureSetROISequence))
 
         # Number of Slices is avg. number slice?
         if hasattr(rtstruct, 'NumberofSlices'):
@@ -66,6 +67,10 @@ def from_dicom_rtstruct(cls, rtstruct_path: str) -> 'StructureSet':
             metadata["RescaleType"] = str(rtstruct.RescaleType)
         if hasattr(rtstruct, 'RescaleSlope'):
             metadata["RescaleSlope"] = str(rtstruct.RescaleSlope)
+        if hasattr(rtstruct, 'PixelSpacing') and hasattr(rtstruct, 'SliceThickness'):
+            pixel_size = copy.copy(rtstruct.PixelSpacing)
+            pixel_size.append(rtstruct.SliceThickness)
+            metadata["PixelSize"] = tuple(pixel_size)
 
         return cls(roi_points, metadata)
         # return cls(roi_points)