histomicsui 1.4.2.dev14__tar.gz → 1.4.2.dev18__tar.gz

{histomicsui-1.4.2.dev14/histomicsui.egg-info → histomicsui-1.4.2.dev18}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: histomicsui
-Version: 1.4.2.dev14
+Version: 1.4.2.dev18
 Summary: Organize, visualize, and analyze histology images.
 Home-page: https://github.com/DigitalSlideArchive/histomicsui
 Author: Kitware, Inc.
@@ -47,9 +47,25 @@ Prerequisites:
 - MongoDB must be installed and running.
 - An appropriate version of Python must be installed.
 
+HistomicsUI uses large_image sources to read different image file formats.  You need to install appropriate sources for the files that will be used.
+
+.. code-block:: bash
+
+  # install all sources from the main repo
+  pip install large-image[sources] --find-links https://girder.github.io/large_image_wheels
+
+or
+
+.. code-block:: bash
+
+  # install openslide and tiff sources
+  pip install large-image-source-tiff large-image-source-openslide --find-links https://girder.github.io/large_image_wheels
+
+Now install the histomicsui package, have Girder build its UI, and start the Girder server.  Note that at Girder may still require an old version of node (12.x) to build correctly -- nvm can be used to manage multiple versions of node.
+
 .. code-block:: bash
 
-  pip install histomicsui[analysis] --find-links https://girder.github.io/large_image_wheels
+  pip install histomicsui[analysis]
   girder build
   girder serve
 

{histomicsui-1.4.2.dev14 → histomicsui-1.4.2.dev18}/README.rst

@@ -23,9 +23,25 @@ Prerequisites:
 - MongoDB must be installed and running.
 - An appropriate version of Python must be installed.
 
+HistomicsUI uses large_image sources to read different image file formats.  You need to install appropriate sources for the files that will be used.
+
+.. code-block:: bash
+
+  # install all sources from the main repo
+  pip install large-image[sources] --find-links https://girder.github.io/large_image_wheels
+
+or
+
+.. code-block:: bash
+
+  # install openslide and tiff sources
+  pip install large-image-source-tiff large-image-source-openslide --find-links https://girder.github.io/large_image_wheels
+
+Now install the histomicsui package, have Girder build its UI, and start the Girder server.  Note that at Girder may still require an old version of node (12.x) to build correctly -- nvm can be used to manage multiple versions of node.
+
 .. code-block:: bash
 
-  pip install histomicsui[analysis] --find-links https://girder.github.io/large_image_wheels
+  pip install histomicsui[analysis]
   girder build
   girder serve
 

{histomicsui-1.4.2.dev14 → histomicsui-1.4.2.dev18}/histomicsui/handlers.py

@@ -115,7 +115,7 @@ def resolveAnnotationGirderIds(event, results, data, possibleGirderIds):
     return True
 
 
-def process_annotations(event):
+def process_annotations(event):  # noqa
     """Add annotations to an image on a ``data.process`` event"""
     results = _itemFromEvent(event, 'AnnotationFile')
     if not results:
@@ -132,7 +132,16 @@ def process_annotations(event):
         logger.error('Could not load models from the database')
         return
     try:
-        data = orjson.loads(File().open(file).read().decode())
+        if file['size'] > 1 * 1024 ** 3:
+            raise Exception('File is larger than will be read into memory.')
+        data = []
+        with File().open(file) as fptr:
+            while True:
+                chunk = fptr.read(1024 ** 2)
+                if not len(chunk):
+                    break
+                data.append(chunk)
+        data = orjson.loads(b''.join(data).decode())
     except Exception:
         logger.error('Could not parse annotation file')
         raise

{histomicsui-1.4.2.dev14 → histomicsui-1.4.2.dev18/histomicsui.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: histomicsui
-Version: 1.4.2.dev14
+Version: 1.4.2.dev18
 Summary: Organize, visualize, and analyze histology images.
 Home-page: https://github.com/DigitalSlideArchive/histomicsui
 Author: Kitware, Inc.
@@ -47,9 +47,25 @@ Prerequisites:
 - MongoDB must be installed and running.
 - An appropriate version of Python must be installed.
 
+HistomicsUI uses large_image sources to read different image file formats.  You need to install appropriate sources for the files that will be used.
+
+.. code-block:: bash
+
+  # install all sources from the main repo
+  pip install large-image[sources] --find-links https://girder.github.io/large_image_wheels
+
+or
+
+.. code-block:: bash
+
+  # install openslide and tiff sources
+  pip install large-image-source-tiff large-image-source-openslide --find-links https://girder.github.io/large_image_wheels
+
+Now install the histomicsui package, have Girder build its UI, and start the Girder server.  Note that at Girder may still require an old version of node (12.x) to build correctly -- nvm can be used to manage multiple versions of node.
+
 .. code-block:: bash
 
-  pip install histomicsui[analysis] --find-links https://girder.github.io/large_image_wheels
+  pip install histomicsui[analysis]
   girder build
   girder serve