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Commit 441de54d authored by Constantin Pape's avatar Constantin Pape
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Fix some path issues and error handling in bdv script

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......@@ -2,7 +2,7 @@
<BasePath type="relative">.</BasePath>
<SequenceDescription>
<ImageLoader format="bdv.hdf5">
<hdf5 type="relative">../rawdata/prospr-6dpf-1-whole-ref-SPM.h5</hdf5>
<hdf5 type="relative">../../rawdata/prospr-6dpf-1-whole-ref-SPM.h5</hdf5>
</ImageLoader>
<ViewSetups>
<ViewSetup>
......
......@@ -207,9 +207,12 @@ prospr-6dpf-1-whole-segmented-RestOfAnimal ../images/prospr-6dpf-1-whole-segment
prospr-6dpf-1-whole-segmented-Stomodeum ../images/prospr-6dpf-1-whole-segmented-Stomodeum.xml
prospr-6dpf-1-whole-segmented-VNC ../images/prospr-6dpf-1-whole-segmented-VNC.xml
prospr-6dpf-1-whole-six12-MED ../images/prospr-6dpf-1-whole-six12-MED.xml
prospr-6dpf-1-whole-ref-SPM ../images/prospr-6dpf-1-whole-ref-SPM.xml
sbem-6dpf-1-whole-segmented-chromatin-labels ../segmentations/sbem-6dpf-1-whole-segmented-chromatin-labels.xml
sbem-6dpf-1-whole-segmented-tissue-labels ../segmentations/sbem-6dpf-1-whole-segmented-tissue-labels.xml
sbem-6dpf-1-whole-segmented-muscle ../segmentations/sbem-6dpf-1-whole-segmented-muscle.xml
sbem-6dpf-1-whole-segmented-cells-labels ../segmentations/sbem-6dpf-1-whole-segmented-cells-labels.xml
sbem-6dpf-1-whole-segmented-nuclei-labels ../segmentations/sbem-6dpf-1-whole-segmented-nuclei-labels.xml
sbem-6dpf-1-whole-segmented-cilia-labels ../segmentations/sbem-6dpf-1-whole-segmented-cilia-labels.xml
sbem-6dpf-1-whole-segmented-ariande-neuropil ../segmentations/sbem-6dpf-1-whole-segmented-ariande-neuropil.xml
sbem-6dpf-1-whole-segmented-cats-neuropil ../segmentations/sbem-6dpf-1-whole-segmented-cats-neuropil.xml
......@@ -2,7 +2,7 @@
<BasePath type="relative">.</BasePath>
<SequenceDescription>
<ImageLoader format="bdv.hdf5">
<hdf5 type="relative">../rawdata/sbem-6dpf-1-whole-segmented-ariande-neuropil.h5</hdf5>
<hdf5 type="relative">../../rawdata/sbem-6dpf-1-whole-segmented-ariande-neuropil.h5</hdf5>
</ImageLoader>
<ViewSetups>
<ViewSetup>
......
......@@ -2,7 +2,7 @@
<BasePath type="relative">.</BasePath>
<SequenceDescription>
<ImageLoader format="bdv.hdf5">
<hdf5 type="relative">../rawdata/sbem-6dpf-1-whole-segmented-cats-neuropil.h5</hdf5>
<hdf5 type="relative">../../rawdata/sbem-6dpf-1-whole-segmented-cats-neuropil.h5</hdf5>
</ImageLoader>
<ViewSetups>
<ViewSetup>
......
......@@ -9,11 +9,12 @@ def add_to_bdv_config(name, path, bdv_config, relative_paths, ref_dir):
h5path = get_h5_path_from_xml(path, return_absolute_path=True)
if not os.path.exists(h5path):
msg = 'Path to h5-file in xml does not exist - %s, %s' % (path, h5path)
return RuntimeError(msg)
raise RuntimeError(msg)
if relative_paths:
path = os.path.relpath(path, ref_dir)
bdv_config[name] = path
return bdv_config
def make_bdv_server_file(folder, out_path, relative_paths=True):
......@@ -29,13 +30,15 @@ def make_bdv_server_file(folder, out_path, relative_paths=True):
if name in privates:
continue
path = os.path.join(folder, 'images', '%s.xml' % name)
add_to_bdv_config(name, path, bdv_config, relative_paths, ref_dir)
bdv_config = add_to_bdv_config(name, path, bdv_config,
relative_paths, ref_dir)
for name in seg_names:
if name in privates:
continue
path = os.path.join(folder, 'segmentations', '%s.xml' % name)
add_to_bdv_config(name, path, bdv_config, relative_paths, ref_dir)
bdv_config = add_to_bdv_config(name, path, bdv_config,
relative_paths, ref_dir)
with open(out_path, 'w') as f:
for name, path in bdv_config.items():
......
......@@ -4,6 +4,7 @@ from .xml_utils import copy_xml_with_newpath, get_h5_path_from_xml
from .sources import get_image_names, get_segmentation_names, get_segmentations
# TODO double check this
def copy_file(xml_in, xml_out):
h5path = get_h5_path_from_xml(xml_in, return_absolute_path=True)
xml_dir = os.path.split(xml_out)[0]
......
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