erp5_wendelin_telecom_ingestion: metadata for nifty images .nii

bt5/erp5_wendelin_telecom_ingestion/ExtensionTemplateItem/portal_components/extension.erp5.external_process_raw_data.py

@@ -115,7 +115,7 @@ def processTextData(file_name, data_array, data_descriptor):
   try:
     json_report = getJSONfromTextFile(file_name)
     data_descriptor.setTextContent(json_report)
-    log("Data Descriptor content saved")
+    log("Data Descriptor text content saved")
   except Exception as e:
     log("Error handling Data Descriptor content: " + str(e))
 
@@ -179,16 +179,43 @@ def processCsvData(file_name, data_array, data_descriptor, delimiter=","):
 def processTsvData(file_name, data_array, data_descriptor):
   processCsvData(file_name, data_array, data_descriptor, delimiter="\t")
 
-def processNiiData(file_name, data_array, data_descriptor):
-  data = {}
-  data["File content sample: "] = "nifti files data processing not available yet."
-  json_data = json.dumps(data)
-  data_descriptor.setTextContent(json_data)
+def processNiiData(file_name, data_array, data_descriptor, gz=False):
+  old_file = file_name
+  file_name = file_name + ".nii.gz" if gz else file_name + ".nii"
+  os.rename(old_file, file_name)
+  try:
+    import nibabel as nib
+    img = nib.load(file_name)
+    data = {}
+    for key in img.header:
+      try:
+        if type(img.header[key]) is np.ndarray:
+          content = img.header[key].tolist()
+          try:
+            if np.isnan(img.header[key]): content = "nan"
+          except:
+            pass
+        else:
+          content = img.header[key]
+        if content == 0: content = "0"
+        json.dumps(content)
+        if content != "":
+          data[key] = content
+      except Exception as e:
+        pass # ignore non serializable info
+    json_data = json.dumps(data)
+    data_descriptor.setTextContent(json_data)
+    log("Data Descriptor nii content saved")
+  except Exception as e:
+    log("Error handling Data Descriptor nii content: " + str(e))
+    raise e
+  finally:
+    os.rename(file_name, old_file)
 
 def processGZData(file_name, data_array, data_descriptor):
-  if data_array.getReference().endswith(".nii/gz"):
-    processNiiData(file_name, data_array, data_descriptor)
-  else:
+  try:
+    processNiiData(file_name, data_array, data_descriptor, gz=True)
+  except:
     raise KeyError("gz")
 
 def processRawData(data_stream, data_array, data_descriptor, reference_extension):
@@ -219,7 +246,7 @@ def processRawData(data_stream, data_array, data_descriptor, reference_extension
     else:
       options["default"](file_name, data_array, data_descriptor)
   except KeyError, e:
-    return "Proccessing for %s data not implemented yet." % reference_extension
+    return "Proccessing for data in this %s not implemented yet." % reference_extension
   except Exception as e:
     return "Error while processing raw data: " + str(e)
   finally:

bt5/erp5_wendelin_telecom_ingestion/ExtensionTemplateItem/portal_components/extension.erp5.external_process_raw_data.xml

@@ -55,6 +55,8 @@
                 <string>W:100,  8: Unused variable \'times\' (unused-variable)</string>
                 <string>W:137,  6: No exception type(s) specified (bare-except)</string>
                 <string>W:173,  8: Unreachable code (unreachable)</string>
+                <string>W:192, 11: Using type() instead of isinstance() for a typecheck. (unidiomatic-typecheck)</string>
+                <string>W:196, 10: No exception type(s) specified (bare-except)</string>
               </tuple>
             </value>
         </item>