From d8fcd34fb8fe9ccc4afbf7ecac11cd0e0a24ca7c Mon Sep 17 00:00:00 2001
From: Constantin Pape <c.pape@gmx.net>
Date: Fri, 21 Jun 2019 10:40:15 +0200
Subject: [PATCH] Add bigdataserver file
---
make_initial_version.py | 7 ++++++-
scripts/files/__init__.py | 1 +
scripts/files/bdv_server.py | 35 +++++++++++++++++++++++++++++++++++
3 files changed, 42 insertions(+), 1 deletion(-)
create mode 100644 scripts/files/bdv_server.py
diff --git a/make_initial_version.py b/make_initial_version.py
index 8bf33d5..ec1a8bc 100755
--- a/make_initial_version.py
+++ b/make_initial_version.py
@@ -6,7 +6,7 @@ from shutil import copyfile
from scripts.files import make_folder_structure
from scripts.export import export_segmentation
from scripts.files import copy_xml_with_abspath, write_simple_xml
-from scripts.files import copy_files_with_pattern
+from scripts.files import copy_files_with_pattern, make_bdv_server_file
from scripts.attributes import make_nucleus_tables, make_cell_tables
@@ -108,6 +108,11 @@ def make_initial_version():
make_tables(folder)
+ # make the bdv server file
+ make_bdv_server_file([os.path.join(folder, 'images'),
+ os.path.join(folder, 'segmentations')],
+ os.path.join(folder, 'misc', 'bdvserver.txt'))
+
if __name__ == '__main__':
make_initial_version()
diff --git a/scripts/files/__init__.py b/scripts/files/__init__.py
index 5088d2a..111cf66 100644
--- a/scripts/files/__init__.py
+++ b/scripts/files/__init__.py
@@ -2,3 +2,4 @@ from .copy_helper import copy_tables, copy_segmentation, copy_static_files
from .copy_helper import copy_files_with_pattern
from .folders import make_folder_structure
from .xml_utils import get_h5_path_from_xml, copy_xml_with_abspath, write_simple_xml
+from .bdv_server import make_bdv_server_file
diff --git a/scripts/files/bdv_server.py b/scripts/files/bdv_server.py
new file mode 100644
index 0000000..dbb63ac
--- /dev/null
+++ b/scripts/files/bdv_server.py
@@ -0,0 +1,35 @@
+import os
+from .xml_utils import get_h5_path_from_xml
+
+
+# TODO enable filtering for files by some patter.
+# e.g. if we don't want to expose the fib dataset to the public yet
+def make_bdv_server_file(folders, out_path):
+ """ Make the bigserver config file from
+ all xmls in folders.
+ """
+ file_list = {}
+ for folder in folders:
+ files = os.listdir(folders)
+ for ff in files:
+ path = os.path.join(folder, ff)
+
+ # only add xmls
+ ext = os.path.splitext(path)[1]
+ if ext != '.xml':
+ continue
+
+ # make sure that the h5path linked in the xml exists
+ 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)
+
+ name = os.path.splitext(ff)[0]
+ file_list[name] = path
+
+ with open(out_path, 'w') as f:
+ for name, path in file_list.items():
+ line = '%s\t%s\n' % (name, path)
+ f.write(line)
--
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