conflict resolved

imgtools/modules/datagraph.py

@@ -59,8 +59,8 @@ def form_graph(self):
         for col in self.df:
             self.df[col] = self.df[col].astype(str)
 
-        # Get reference_rs information from RTDOSE-RTPLAN connections    
-        df_filter = pd.merge(self.df, self.df[["instance_uid","reference_rs"]], 
+        #Get reference_rs information from RTDOSE-RTPLAN connections    
+        df_filter = pd.merge(self.df, self.df[["instance_uid","reference_rs"]].apply(lambda x: x.astype(str), axis=1), 
                              left_on="reference_pl", 
                              right_on="instance_uid", 
                              how="left")

imgtools/utils/nifti_to_dicom.py

@@ -0,0 +1,46 @@
+import SimpleITK as sitk
+from rt_utils import RTStructBuilder
+import pydicom
+import logging
+import glob
+import numpy as np
+import os
+
+'''You need to install rt_utils first using 
+    pip install rt_utils'''
+
+
+def segmentations_to_dicom(save_path:str,orig_series_info:dict, segmentation:sitk.Image,segmentations_labels:dict,
+                             color_list=None, rtstruct_basefilename='rtstruct.dcm'):
+    """
+    This function takes a list of the original dicom data, moves it to the save_path and creates a corresponding rt_struct
+    @param image_set_name: name of the image set used to create the dicom sub directory
+    @param save_path: directory to save dicom data
+    @param orig_series_info: original series info see @get_dicom_series_dict_pyd
+    @param segmentation: the image containing integer segmentation data
+    @param segmentations_labels: a dictionary with segmentation label information mapping ints in @segmentation to label
+    name e.g. {1: 'Bladder', 2: 'Rectum', 3: 'Sigmoid', 4: 'SmallBowel'}
+    @return:
+    """
+    _logger=logging.getLogger(__name__)
+    #make output dir
+    if not os.path.isdir(save_path):
+        _logger.warning(f'Making path: {save_path}')
+        os.makedirs(save_path)
+
+
+    im_array = sitk.GetArrayFromImage(segmentation)
+    rtstruct = RTStructBuilder.create_new(dicom_series_path=orig_series_info)
+    for i,(key,name) in enumerate(segmentations_labels.items()):
+        mask = np.where(im_array!=key,0,im_array)
+        mask = np.array(mask,dtype=bool)
+        mask = np.transpose(mask, (1,2,0))
+
+        index = i%len(color_list)
+
+        rtstruct.add_roi(mask=mask, name=name, color=color_list[index],approximate_contours=False)
+
+
+    rtstruct_name = os.path.join(save_path,rtstruct_basefilename)
+    _logger.info(f'Saving rtstruct data: {rtstruct_name}')
+    rtstruct.save(rtstruct_name)

setup.py

@@ -8,7 +8,7 @@
 
 setup(
     name="med-imagetools",
-    version="1.1.5",
+    version="1.1.6",
     author="Sejin Kim, Michal Kazmierski, Kevin Qu, Vishwesh Ramanathan, Benjamin Haibe-Kains",
     author_email="benjamin.haibe.kains@utoronto.ca",
     description="Transparent and reproducible image processing pipelines in Python.",