large-image-source-dicom 1.27.2.dev8__tar.gz → 1.27.2.dev12__tar.gz

{large-image-source-dicom-1.27.2.dev8 → large-image-source-dicom-1.27.2.dev12}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: large-image-source-dicom
-Version: 1.27.2.dev8
+Version: 1.27.2.dev12
 Summary: A DICOM tilesource for large_image.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.

{large-image-source-dicom-1.27.2.dev8 → large-image-source-dicom-1.27.2.dev12}/large_image_source_dicom/assetstore/dicomweb_assetstore_adapter.py

@@ -139,41 +139,14 @@ class DICOMwebAssetstoreAdapter(AbstractAssetstoreAdapter):
     def downloadFile(self, file, offset=0, headers=True, endByte=None,
                      contentDisposition=None, extraParameters=None, **kwargs):
 
-        from dicomweb_client.web import _Transaction
-
-        dicom_uids = file['dicom_uids']
-        study_uid = dicom_uids['study_uid']
-        series_uid = dicom_uids['series_uid']
-        instance_uid = dicom_uids['instance_uid']
-
-        client = _create_dicomweb_client(self.assetstore_meta)
-
         if headers:
             setResponseHeader('Accept-Ranges', 'bytes')
             self.setContentHeaders(file, offset, endByte, contentDisposition)
 
-        # Create the URL
-        url = client._get_instances_url(
-            _Transaction.RETRIEVE,
-            study_uid,
-            series_uid,
-            instance_uid,
-        )
-
-        # Build the headers
-        transfer_syntax = '*'
-        accept_parts = [
-            'multipart/related',
-            'type="application/dicom"',
-            f'transfer-syntax={transfer_syntax}',
-        ]
-        request_headers = {
-            'Accept': '; '.join(accept_parts),
-        }
-
         def stream():
             # Perform the request
-            response = client._http_get(url, headers=request_headers, stream=True)
+            # Try a single-part download first. If that doesn't work, do multipart.
+            response = self._request_retrieve_instance_prefer_singlepart(file)
 
             bytes_read = 0
             for chunk in self._stream_retrieve_instance_response(response):
@@ -203,6 +176,76 @@ class DICOMwebAssetstoreAdapter(AbstractAssetstoreAdapter):
 
         return stream
 
+    def _request_retrieve_instance_prefer_singlepart(self, file, transfer_syntax='*'):
+        # Try to perform a singlepart request. If it fails, perform a multipart request
+        # instead.
+        response = None
+        try:
+            response = self._request_retrieve_instance(file, multipart=False,
+                                                       transfer_syntax=transfer_syntax)
+        except requests.HTTPError:
+            # If there is an HTTPError, the server might not accept single-part requests...
+            pass
+
+        if self._is_singlepart_response(response):
+            return response
+
+        # Perform the multipart request instead
+        return self._request_retrieve_instance(file, transfer_syntax=transfer_syntax)
+
+    def _request_retrieve_instance(self, file, multipart=True, transfer_syntax='*'):
+        # Multipart requests are officially supported by the DICOMweb standard.
+        # Singlepart requests are not officially supported, but they are easier
+        # to work with.
+        # Google Healthcare API support it.
+        # See here: https://cloud.google.com/healthcare-api/docs/dicom#dicom_instances
+
+        # Create the URL
+        client = _create_dicomweb_client(self.assetstore_meta)
+        url = self._create_retrieve_instance_url(client, file)
+
+        # Build the headers
+        headers = {}
+        if multipart:
+            # This is officially supported by the DICOMweb standard.
+            headers['Accept'] = '; '.join((
+                'multipart/related',
+                'type="application/dicom"',
+                f'transfer-syntax={transfer_syntax}',
+            ))
+        else:
+            # This is not officially supported by the DICOMweb standard,
+            # but it is easier to work with, and some servers such as
+            # Google Healthcare API support it.
+            # See here: https://cloud.google.com/healthcare-api/docs/dicom#dicom_instances
+            headers['Accept'] = f'application/dicom; transfer-syntax={transfer_syntax}'
+
+        return client._http_get(url, headers=headers, stream=True)
+
+    def _create_retrieve_instance_url(self, client, file):
+        from dicomweb_client.web import _Transaction
+
+        dicom_uids = file['dicom_uids']
+        study_uid = dicom_uids['study_uid']
+        series_uid = dicom_uids['series_uid']
+        instance_uid = dicom_uids['instance_uid']
+
+        return client._get_instances_url(
+            _Transaction.RETRIEVE,
+            study_uid,
+            series_uid,
+            instance_uid,
+        )
+
+    def _stream_retrieve_instance_response(self, response):
+        # Check if the original request asked for multipart data
+        if 'multipart/related' in response.request.headers.get('Accept', ''):
+            yield from self._stream_dicom_multipart_response(response)
+        else:
+            # The content should *only* contain the DICOM file
+            with response:
+                yield from response.iter_content(BUF_SIZE)
+
     def _extract_media_type_and_boundary(self, response):
         content_type = response.headers['content-type']
         media_type, *ct_info = (ct.strip() for ct in content_type.split(';'))
@@ -215,7 +258,7 @@ class DICOMwebAssetstoreAdapter(AbstractAssetstoreAdapter):
 
         return media_type, boundary
 
-    def _stream_retrieve_instance_response(self, response):
+    def _stream_dicom_multipart_response(self, response):
         # The first part of this function was largely copied from dicomweb-client's
         # _decode_multipart_message() function. But we can't use that function here
         # because it relies on reading the whole DICOM file into memory. We want to
@@ -307,6 +350,50 @@ class DICOMwebAssetstoreAdapter(AbstractAssetstoreAdapter):
             msg = 'Failed to find ending boundary in response content'
             raise ValueError(msg)
 
+    def _infer_file_size(self, file):
+        # Try various methods to infer the file size, without streaming the
+        # whole file. Returns the file size if successful, or `None` if unsuccessful.
+        if file.get('size') is not None:
+            # The file size was already determined.
+            return file['size']
+
+        # Only method currently is inferring from single-part content_length
+        return self._infer_file_size_singlepart_content_length(file)
+
+    def _is_singlepart_response(self, response):
+        if response is None:
+            return False
+
+        content_type = response.headers.get('Content-Type')
+        return (
+            response.status_code == 200 and
+            not any(x in content_type for x in ('multipart/related', 'boundary'))
+        )
+
+    def _infer_file_size_singlepart_content_length(self, file):
+        # First, try to see if single-part requests work, and if the Content-Length
+        # is returned. This works for Google Healthcare API.
+        try:
+            response = self._request_retrieve_instance(file, multipart=False)
+        except requests.HTTPError:
+            # If there is an HTTPError, the server might not accept single-part requests...
+            return
+
+        if not self._is_singlepart_response(response):
+            # Does not support single-part requests...
+            return
+
+        content_length = response.headers.get('Content-Length')
+        if not content_length:
+            # The server did not return a Content-Length
+            return
+
+        try:
+            # The DICOM file size is equal to the Content-Length
+            return int(content_length)
+        except ValueError:
+            return
+
     def importData(self, parent, parentType, params, progress, user, **kwargs):
         """
         Import DICOMweb WSI instances from a DICOMweb server.
@@ -408,7 +495,10 @@ class DICOMwebAssetstoreAdapter(AbstractAssetstoreAdapter):
                     'instance_uid': instance_uid,
                 }
                 file['imported'] = True
-                File().save(file)
+
+                # Try to infer the file size without streaming, if possible.
+                file['size'] = self._infer_file_size(file)
+                file = File().save(file)
 
             items.append(item)
 
@@ -420,16 +510,23 @@ class DICOMwebAssetstoreAdapter(AbstractAssetstoreAdapter):
 
     def getFileSize(self, file):
         # This function will compute the size of the DICOM file (a potentially
-        # expensive operation, since it may have to stream the whole file),
-        # and cache the result in file['size'].
+        # expensive operation, since it may have to stream the whole file).
+        # The caller is expected to cache the result in file['size'].
         # This function is called when the size is needed, such as the girder
         # fuse mount code, and range requests.
         if file.get('size') is not None:
             # It has already been computed once. Return the cached size.
             return file['size']
 
+        # Try to infer the file size without streaming, if possible.
+        size = self._infer_file_size(file)
+        if size:
+            return size
+
+        # We must stream the whole file to get the file size...
         size = 0
-        for chunk in self.downloadFile(file, headers=False)():
+        response = self._request_retrieve_instance_prefer_singlepart(file)
+        for chunk in self._stream_retrieve_instance_response(response):
             size += len(chunk)
 
         # This should get cached in file['size'] in File().updateSize().

{large-image-source-dicom-1.27.2.dev8 → large-image-source-dicom-1.27.2.dev12}/large_image_source_dicom.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: large-image-source-dicom
-Version: 1.27.2.dev8
+Version: 1.27.2.dev12
 Summary: A DICOM tilesource for large_image.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.

large-image-source-dicom-1.27.2.dev12/large_image_source_dicom.egg-info/requires.txt

@@ -0,0 +1,5 @@
+large-image>=1.27.2.dev12
+wsidicom>=0.9.0
+
+[girder]
+girder-large-image>=1.27.2.dev12

large-image-source-dicom-1.27.2.dev8/large_image_source_dicom.egg-info/requires.txt

@@ -1,5 +0,0 @@
-large-image>=1.27.2.dev8
-wsidicom>=0.9.0
-
-[girder]
-girder-large-image>=1.27.2.dev8