Add script for legacy platy-browser export

legacy_export.py

+import os
+# from pathlib import Path
+from shutil import copyfile
+
+
+# TODO need to replace the name in xml to make this work out of the box
+def export_segmentation(folder, name, dest_folder, out_name):
+    seg_file = os.path.join(folder, 'segmentations', '%s.h5' % name)
+    xml_file = os.path.join(folder, 'segmentations', '%s.xml' % name)
+    table_file = os.path.join(folder, 'tables', name, 'default.csv')
+    assert os.path.exists(seg_file)
+    assert os.path.exists(xml_file)
+    assert os.path.exists(table_file), table_file
+
+    seg_out = os.path.join(dest_folder, '%s.h5' % out_name)
+    print("Copying segmentation from", seg_file, "to", seg_out)
+    copyfile(seg_file, seg_out)
+
+    xml_out = os.path.join(dest_folder, '%s.xml' % out_name)
+    print("Copying xml from", xml_file, "to", xml_out)
+    copyfile(xml_file, xml_out)
+
+    table_out = os.path.join(dest_folder, 'tables', '%s.csv' % out_name)
+    print("Copying table from", table_file, "to", table_out)
+    copyfile(table_file, table_out)
+
+
+def export_tag(tag, export_cells=False, export_cilia=False):
+    tag_folder = './data/%s' % tag
+    assert os.path.exists(tag_folder)
+
+    dest_folder = '/g/arendt/EM_6dpf_segmentation/EM-Prospr'
+
+    if export_cells:
+        name = 'sbem-6dpf-1-whole-segmented-cells-labels'
+        out_name = 'em-segmented-cells-new-labels'
+        export_segmentation(tag_folder, name, dest_folder, out_name)
+
+    if export_cilia:
+        name = 'sbem-6dpf-1-whole-segmented-cilia-labels'
+        out_name = 'em-segmented-cilia-labels'
+        export_segmentation(tag_folder, name, dest_folder, out_name)
+
+
+if __name__ == '__main__':
+    # export_tag('0.1.1', export_cells=True)
+    export_tag('0.1.0', export_cilia=True)