From 441de54dea6970f7ae613f7bf59075f3a1c0295e Mon Sep 17 00:00:00 2001
From: Constantin Pape <constantin.pape@iwr.uni-heidelberg.de>
Date: Fri, 16 Aug 2019 15:47:11 +0200
Subject: [PATCH] Fix some path issues and error handling in bdv script
---
data/0.3.0/images/prospr-6dpf-1-whole-ref-SPM.xml | 2 +-
data/0.3.0/misc/bdv_server.txt | 3 +++
.../sbem-6dpf-1-whole-segmented-ariande-neuropil.xml | 2 +-
.../sbem-6dpf-1-whole-segmented-cats-neuropil.xml | 2 +-
scripts/files/bdv_server.py | 9 ++++++---
scripts/files/copy_helper.py | 1 +
6 files changed, 13 insertions(+), 6 deletions(-)
diff --git a/data/0.3.0/images/prospr-6dpf-1-whole-ref-SPM.xml b/data/0.3.0/images/prospr-6dpf-1-whole-ref-SPM.xml
index 37d5e72..889b518 100644
--- a/data/0.3.0/images/prospr-6dpf-1-whole-ref-SPM.xml
+++ b/data/0.3.0/images/prospr-6dpf-1-whole-ref-SPM.xml
@@ -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>
diff --git a/data/0.3.0/misc/bdv_server.txt b/data/0.3.0/misc/bdv_server.txt
index acc8bfb..7b5323e 100644
--- a/data/0.3.0/misc/bdv_server.txt
+++ b/data/0.3.0/misc/bdv_server.txt
@@ -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
diff --git a/data/0.3.0/segmentations/sbem-6dpf-1-whole-segmented-ariande-neuropil.xml b/data/0.3.0/segmentations/sbem-6dpf-1-whole-segmented-ariande-neuropil.xml
index 2bab095..5f99490 100644
--- a/data/0.3.0/segmentations/sbem-6dpf-1-whole-segmented-ariande-neuropil.xml
+++ b/data/0.3.0/segmentations/sbem-6dpf-1-whole-segmented-ariande-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>
diff --git a/data/0.3.0/segmentations/sbem-6dpf-1-whole-segmented-cats-neuropil.xml b/data/0.3.0/segmentations/sbem-6dpf-1-whole-segmented-cats-neuropil.xml
index 008437a..270aa82 100644
--- a/data/0.3.0/segmentations/sbem-6dpf-1-whole-segmented-cats-neuropil.xml
+++ b/data/0.3.0/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-cats-neuropil.h5</hdf5>
+ <hdf5 type="relative">../../rawdata/sbem-6dpf-1-whole-segmented-cats-neuropil.h5</hdf5>
</ImageLoader>
<ViewSetups>
<ViewSetup>
diff --git a/scripts/files/bdv_server.py b/scripts/files/bdv_server.py
index 39eb1b0..df40515 100644
--- a/scripts/files/bdv_server.py
+++ b/scripts/files/bdv_server.py
@@ -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():
diff --git a/scripts/files/copy_helper.py b/scripts/files/copy_helper.py
index db30de4..f9fba57 100644
--- a/scripts/files/copy_helper.py
+++ b/scripts/files/copy_helper.py
@@ -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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