From 56ff818e9d8dcf81b39d68041aadd1f67bbf8ded Mon Sep 17 00:00:00 2001
From: "Olivier J.N. Bertrand" <olivier.bertrand@uni-bielefeld.de>
Date: Tue, 6 Nov 2018 14:59:23 +0100
Subject: [PATCH] Improve loading of the image in database
---
navipy/database/__init__.py | 14 ++++++++++++++
navipy/scripts/blend_alongtraj.py | 14 ++++++++++++--
navipy/scripts/blendnavipy.py | 18 ++++++++++++++----
3 files changed, 40 insertions(+), 6 deletions(-)
diff --git a/navipy/database/__init__.py b/navipy/database/__init__.py
index bf3bd60..973fa1d 100644
--- a/navipy/database/__init__.py
+++ b/navipy/database/__init__.py
@@ -704,6 +704,20 @@ class DataBase():
WHERE (rowid=?)
""".format(tablename), (rowid,))
image = self.db_cursor.fetchone()[0]
+ # Check image size
+ # and try to correct it whenever possible
+ if not isinstance(image, np.ndarray):
+ msg = 'image must be np.array'
+ self._logger.exception(msg)
+ raise TypeError(msg)
+ if len(image.shape) > 3:
+ if np.all(image.shape[3:] == np.ones_like(image.shape[3:])):
+ image = image[:, :, :, 0] # Other dim are useless
+ if len(image.shape) != 3:
+ msg = 'image should be 3D array'
+ msg += 'image size is {}'.format(image.shape)
+ self._logger.exception(msg)
+ raise Exception(msg)
# Read cmaxminrange
tablename = 'normalisation'
cmaxminrange = pd.read_sql_query(
diff --git a/navipy/scripts/blend_alongtraj.py b/navipy/scripts/blend_alongtraj.py
index fafd2ea..a4cf7d1 100644
--- a/navipy/scripts/blend_alongtraj.py
+++ b/navipy/scripts/blend_alongtraj.py
@@ -56,7 +56,12 @@ def parser_blend_alongtraj():
type=str,
default=None,
help=arghelp)
-
+ arghelp = 'To ignore the autocheck of python version'
+ arghelp += 'and blender'
+ parser.add_argument('--ignorepycheck',
+ default=0,
+ help=arghelp,
+ action='count')
return parser
@@ -100,14 +105,19 @@ def main():
tfile.write('except Exception:\n'.encode(encoding))
tfile.write(' sys.exit(1)\n'.encode(encoding))
tfile.seek(0)
+ if args.ignorepycheck == 0:
+ ignorepyversion = ''
+ else:
+ ignorepyversion = '--ignorepycheck '
- command = 'blendnavipy --background '
+ command = 'blendnavipy --background {}'.format(ignorepyversion)
command += '--blender-world {} --python-script {}'
command = command.format(args.blender_world, tfile.name)
if args.blender_command is not None:
command += ' --blender-command {}'.format(args.blender_command)
for _ in range(args.verbose):
command += ' -v'
+ print(command)
os.system(command)
diff --git a/navipy/scripts/blendnavipy.py b/navipy/scripts/blendnavipy.py
index 8837f87..ab2cf95 100644
--- a/navipy/scripts/blendnavipy.py
+++ b/navipy/scripts/blendnavipy.py
@@ -82,6 +82,13 @@ def parser_blendnavipy():
action='count',
default=0,
help=arghelp)
+
+ arghelp = 'To ignore the autocheck of python version'
+ arghelp += 'and blender'
+ parser.add_argument('--ignorepycheck',
+ default=0,
+ help=arghelp,
+ action='count')
return parser
@@ -120,14 +127,17 @@ def main():
with tempfile.NamedTemporaryFile() as tfile:
# Start of file
tfile.write(header.encode(encoding))
+ # Check blender version
tfile.write('# check blender version\n'.encode(encoding))
tfile.write('import sys \n'.encode(encoding))
tfile.write('import os \n'.encode(encoding))
- for line in inspect.getsourcelines(blender_version)[0]:
+ if args.ignorepycheck == 0:
+ for line in inspect.getsourcelines(blender_version)[0]:
+ tfile.write(line.encode(encoding))
+ tfile.write('\n\n'.encode(encoding))
+ line = 'blender_version({})\n'.format(pyver)
tfile.write(line.encode(encoding))
- tfile.write('\n\n'.encode(encoding))
- line = 'blender_version({})\n'.format(pyver)
- tfile.write(line.encode(encoding))
+ # Load venv
if venv_path is not None:
tfile.write(
'# activate virtualenv within blender\n'.encode(encoding))
--
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