Load dicom

https://www.notion.so/qim-dtu/DICOM-data-loader-a9c9bea7021b472ca63d8bbab08ca696?pvs=4

Ability to load DICOM files or folders.

qim3d/io/load.py

@@ -445,12 +445,36 @@ class DataLoader:
         Args:
             path (str): Path to file
         """
-        dcm_data = pydicom.dcmread(path)
+        if self.virtual_stack:
+            defer_size = '2 MB'
+        else:
+            defer_size = None
+            
+        dcm_data = pydicom.dcmread(path, defer_size=defer_size)
         
         if self.return_metadata:
             return dcm_data.pixel_array, dcm_data
         else:
             return dcm_data.pixel_array
+    
+    def load_dicom_dir(self, path):
+        """ Load a directory of DICOM files into a numpy 3d array
+
+        Args:
+            path (str): Directory path
+        """ 
+        # loop over all .dcm files in the directory
+        files = [f for f in os.listdir(path) if f.endswith('.dcm')]
+        files.sort()
+        # dicom_list contains the dicom objects with metadata
+        dicom_list = [pydicom.dcmread(os.path.join(path, f)) for f in files]
+        # vol contains the pixel data
+        vol = np.stack([dicom.pixel_array for dicom in dicom_list], axis=0)
+        
+        if self.return_metadata:
+            return vol, dicom_list
+        else:
+            return vol
         
 
     def load(self, path):
@@ -499,7 +523,11 @@ class DataLoader:
 
         # Load a directory
         elif os.path.isdir(path):
-            return self.load_tiff_stack(path)
+            # load dicom if directory contains dicom files else load tiff stack as default
+            if any([f.endswith('.dcm') for f in os.listdir(path)]):
+                return self.load_dicom_dir(path)
+            else:
+                return self.load_tiff_stack(path)
 
         # Fails
         else: