Merge branch 'master' into twomarkerorient

README.md

@@ -66,6 +66,18 @@ python setup.py install
 ```
 
 ## Blender-python version
+Navipy can be interfaced with blender. It is highly recommended to use the same version of packages of blender when doing so, in order to reduce problem of compatibility.
+To determine the packages that you will need, you can run the script: `navipy/script/check_blender_versions_pip.py` in blender or via commandline:
+
+```
+blender -b -P check_blender_versions_pip.py
+```
+
+It will create a textfile containing all packages used by blender. They can be installed in your virtualenvironment (prior to navipy) by doing:
+```
+pip install -r requirement.txt
+```
+
 | Blender version | Python version |
 | --------------- | -------------- |
 | 2.79b           | 3.5.3          |

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(

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)
 
 

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))

navipy/scripts/check_blender_versions_pip.py

+"""
+List all installed packages in a python installation
+by using pip.
+
+It can be used to install a virtual environment, so that it matches
+another installation (for example blender)
+"""
+import pip
+
+
+installed_packages = pip.get_installed_distributions()
+installed_packages = sorted(["%s==%s" % (i.key, i.version)
+                             for i in installed_packages])
+with open('requirement.txt', 'w') as cfile:
+    for line in installed_packages:
+        print(line)
+        cfile.write(line+'\n')

navipy/trajectories/__init__.py

@@ -792,6 +792,7 @@ series.
                 fig = plt.figure()
                 ax = fig.add_subplot(111, projection='3d')
             elif len(plotcoords) == 2:
+                fig = plt.figure()
                 ax = fig.add_subplot(111)
         if (len(plotcoords) != 2) and (len(plotcoords) != 3):
             msg = 'plotcoords need to contains 2 or 3 elements'