Merge pull request #8 from joshicola/GEAR-2399/load_paired_files

Support for mhd:raw, hdr:img

FlywheelConnect/flywheel_connect.py

@@ -266,8 +266,6 @@ def onProjectSelected(self, item):
                 self.tree_management.source_model.removeRows(0, tree_rows)
             self.loadFilesButton.enabled = False
 
-            self.segmentationButton.enabled = False
-
     def is_compressed_dicom(self, file_path, file_type):
         """
         Check file_path and file_type for a flywheel compressed dicom archive.

FlywheelConnect/management/fw_container_items.py

@@ -5,6 +5,11 @@
 from PythonQt.QtCore import Qt
 from qt import QAbstractItemView
 
+# Common paired file types
+PAIRED_FILE_TYPES = {
+    "mhd": "raw",
+    "hdr": "img"
+}
 
 class FolderItem(QtGui.QStandardItem):
     """
@@ -365,6 +370,33 @@ def _get_cache_path(self):
         file_path /= self.container.name
         return file_path
 
+    def _is_paired_type(self):
+        """
+        Determine if this file is of a paired type.
+
+        Returns:
+            bool: True or False of paired type.
+        """        
+        return self.container.name.split(".")[-1] in PAIRED_FILE_TYPES.keys()
+
+    def _get_paired_file(self):
+        """
+        Get the pair of current file, if exists
+
+        Returns:
+            str: Name of paired file
+        """        
+        file_parent = self.parent_item.parent().container
+        fl_ext = self.container.name.split(".")[-1]
+        paired_ext = PAIRED_FILE_TYPES[fl_ext]
+        paired_file_name = self.container.name[:-len(fl_ext)] + paired_ext
+
+        # file definition is retrieved or a None is returned.
+        if file_parent.get_file(paired_file_name):
+            return paired_file_name
+        else:
+            return None
+
     def _is_cached(self):
         """
         Check if file is cached.
@@ -383,11 +415,20 @@ def _add_to_cache(self):
         """
         file_path = self._get_cache_path()
         file_parent = self.parent_item.parent().container
+
         if not file_path.exists():
             if not file_path.parents[0].exists():
                 os.makedirs(file_path.parents[0])
             file_parent.download_file(self.file.name, str(file_path))
             self.icon_path = "Resources/Icons/file_cached.png"
             self.setToolTip("File is cached.")
             self._set_icon()
+        # Check if this file is of a paired type
+        if self._is_paired_type():
+            # attempt to find the paired type
+            paired_file_name = self._get_paired_file()
+            # if found, download the adjoining pair into original directory
+            if paired_file_name:
+                file_parent.download_file(paired_file_name, str(file_path.parents[0]/paired_file_name))
+
         return file_path, self.file_type

INSTALLATION.md

@@ -11,3 +11,6 @@ Follow these steps to run a local copy of the extension:
 1. Clone this github repository into a convenient location
 2. Add the FlywheelConnect subfolder of the repository as an additional module path (in menu: Edit / Application settings -> Modules -> Additional module paths; either drag-and-drop the FlywheelConnect folder to the path list, or click the double-arrow button and then click Add and select the FlywheelConnect folder)
 3. Restart the application
+
+## Bonus
+In place of (2) above, install the DeveloperToolsForExtensions Extension and locate the FlywheelConnect folder in the Extension Wizard.

README.md

@@ -6,7 +6,7 @@ A 3D Slicer Extension to view, select, and download images from a Flywheel insta
 Flywheel is a comprehensive data management solutions for life sciences and imaging research.
 More details at [https://flywheel.io/](https://flywheel.io/).
 
-The Flywheel Connect 3D Slicer Extension is now in the [3D Slicer Extension Catalog](https://slicer.kitware.com/midas3/slicerappstore/extension/view?extensionId=460488) and available through the [3D Slicer Extensions Manager](https://slicer.readthedocs.io/en/latest/user_guide/extensions_manager.html) for direct installation.
+The Flywheel Connect 3D Slicer Extension is now in the [3D Slicer Extension Catalog](https://extensions.slicer.org/view/flywheel_connect/30117/linux) and available through the [3D Slicer Extensions Manager](https://slicer.readthedocs.io/en/latest/user_guide/extensions_manager.html) for direct installation.
 
 ## Usage Instructions
 
@@ -39,3 +39,6 @@ The interface is shown below. Notable areas are commented on:
 * H) Load all selected files. Files that are Slicer-supported data formats (Images and Models) will be loaded. This will only be enabled if files are selected.
 * I) Upload derived files to Flywheel Analysis or Container files. This will only be enabled if a single valid Flywheel Container is selected.
 * H) If checked, indicates that derived files should be uploaded to Flywheel as Analysis output under the selected Container.
+
+## ToDo
+- [ ] Ensure that a created analysis downloads the necessary files to the cache if they are not already there.