Merge pull request #1195 from girder/convert-multiframe

Fix converting multiframe files that vips reads as single frame
girder · Jun 8, 2023 · 33147c2 · 33147c2
2 parents 9408b52 + 5908989
commit 33147c2
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Showing 5 changed files with 18 additions and 3 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,9 @@
 - Refactor reading the .large_image_config.yaml file on the girder client ([#1193](../../pull/1193))
 - Refactor of the which-folders-have-annotations pipeline ([#1194](../../pull/1194))
 
+### Bug Fixes
+- Fix an issue converting multiframe files that vips reads as single frame  ([#1195](../../pull/1195))
+
 ## 1.22.2
 
 ### Changes

diff --git a/girder/girder_large_image/web_client/templates/largeImage_fileAction.pug b/girder/girder_large_image/web_client/templates/largeImage_fileAction.pug
@@ -7,5 +7,5 @@ else if largeImage && largeImage.expected === true
   a.g-large-image-expected(title="A large image file is being generated")
     i.icon-picture
 else if !largeImage || !largeImage.fileId
-  a.g-large-image-create(title="Use this file for a large image")
+  a.g-large-image-create(title="Use this file for a large image.  Ctrl-click to force converting the image before using it")
     i.icon-picture
diff --git a/girder/girder_large_image/web_client/views/fileList.js b/girder/girder_large_image/web_client/views/fileList.js
@@ -53,7 +53,7 @@ wrap(FileListWidget, 'render', function (render) {
         restRequest({
             type: 'POST',
             url: 'item/' + this.parentItem.id + '/tiles',
-            data: {fileId: fileId, notify: true},
+            data: {fileId: fileId, notify: true, force: !!(e.originalEvent || {}).ctrlKey},
             error: function (error) {
                 if (error.status !== 0) {
                     events.trigger('g:alert', {

diff --git a/test/test_converter.py b/test/test_converter.py
@@ -1,6 +1,7 @@
 import json
 import os
 import shutil
+import sys
 
 import large_image_converter
 import large_image_converter.__main__ as main
@@ -314,3 +315,12 @@ def testConvertFromTestSourceFrameArray(tmpdir):
     assert len(metadata['frames']) == 6
     info = tifftools.read_tiff(outputPath)
     assert len(info['ifds']) == 6
+
+
+@pytest.mark.skipif(sys.version_info < (3, 7), reason='requires python >= 3.7 for the test image')
+def testConvertImageJ(tmpdir):
+    imagePath = datastore.fetch('synthetic_imagej.tiff')
+    outputPath = os.path.join(tmpdir, 'out.tiff')
+    large_image_converter.convert(imagePath, outputPath, compression='jpeg', quality=50)
+    info = tifftools.read_tiff(outputPath)
+    assert len(info['ifds']) == 44
diff --git a/utilities/converter/large_image_converter/__init__.py b/utilities/converter/large_image_converter/__init__.py
@@ -924,7 +924,9 @@ def convert(inputPath, outputPath=None, **kwargs):  # noqa: C901
             lidata = _data_from_large_image(inputPath, tempPath, **kwargs)
             logger.log(logging.DEBUG - 1, 'large_image information for %s: %r',
                        inputPath, lidata)
-            if not is_vips(inputPath) and lidata:
+            if lidata and (not is_vips(inputPath) or (
+                    len(lidata['metadata'].get('frames', [])) >= 2 and
+                    not _is_multiframe(inputPath))):
                 _convert_large_image(inputPath, outputPath, tempPath, lidata, **kwargs)
             elif _is_multiframe(inputPath):
                 _generate_multiframe_tiff(inputPath, outputPath, tempPath, lidata, **kwargs)