Merge branch 'command-line' of git://github.com/xmartlabs/invesalius3 into xmartlabs-command-line

Thiago Franco de Moraes
2 parents 9abcd9d1 34cd93f5
Showing 4 changed files with 98 additions and 8 deletions Show diff stats
.dockerignore
Dockerfile
app.py
invesalius/control.py
@@ -0,0 +1,3 @@
+.git*
+.python-version
+Dockerfile
@@ -0,0 +1,31 @@
+FROM ubuntu:16.04
+
+RUN apt-get update
+RUN apt-get install -y \
+    cython \
+    python-concurrent.futures \
+    python-gdcm \
+    python-matplotlib \
+    python-nibabel \
+    python-numpy \
+    python-pil \
+    python-psutil \
+    python-scipy \
+    python-serial \
+    python-skimage \
+    python-vtk6 \
+    python-vtkgdcm \
+    python-wxgtk3.0 \
+    xvfb # For a virtual X server.
+
+RUN apt-get install -y locales
+RUN locale-gen en_US.UTF-8
+ENV LANG en_US.UTF-8
+ENV LANGUAGE en_US:en
+ENV LC_ALL en_US.UTF-8
+
+WORKDIR /usr/local/app
+
+COPY . .
+
+RUN python setup.py build_ext --inplace
@@ -24,6 +24,7 @@ import optparse as op
 import os
 import sys
 import shutil
+import traceback
  
 if sys.platform == 'win32':
     import _winreg
@@ -245,6 +246,13 @@ def parse_comand_line():
     parser.add_option("-i", "--import",
                       action="store",
                       dest="dicom_dir")
+
+    parser.add_option("-s", "--save",
+                      help="To save the project after an import.")
+
+    parser.add_option("-a", "--export-to-all",
+                      help="To open a project and export it to STL for all mask presets.")
+
     options, args = parser.parse_args()
  
     # If debug argument...
@@ -256,23 +264,65 @@ def parse_comand_line():
     if options.dicom_dir:
         import_dir = options.dicom_dir
         Publisher.sendMessage('Import directory', import_dir)
+
+        if options.save:
+            Publisher.sendMessage('Save project', os.path.abspath(options.save))
+            exit(0)
+
+        check_for_exporting(options)
+
         return True
  
     # Check if there is a file path somewhere in what the user wrote
     # In case there is, try opening as it was a inv3
     else:
-        i = len(args)
-        while i:
-            i -= 1
-            file = args[i]
-            if os.path.isfile(file):
-                path = os.path.abspath(file)
-                Publisher.sendMessage('Open project', path)
-                i = 0
+        for arg in reversed(args):
+            if os.path.isfile(arg):
+                path_ = os.path.abspath(arg)
+                Publisher.sendMessage('Open project', path_)
+
+                check_for_exporting(options)
+
                 return True
     return False
  
  
+def check_for_exporting(options):
+    if options.export_to_all:
+        try:
+            method = {
+                'algorithm': 'Default',
+                'options': {},
+            }
+
+            import invesalius.constants as const
+            from invesalius.project import Project
+
+            for threshold_name, threshold_range in Project().presets.thresh_ct.iteritems():
+                if isinstance(threshold_range[0], int):
+                    Publisher.sendMessage('Set threshold values', threshold_range)
+
+                    srf_options = {
+                        'index': 0,
+                        'name': '',
+                        'quality': _('Optimal *'),
+                        'fill': False,
+                        'keep_largest': False,
+                        'overwrite': False,
+                    }
+                    Publisher.sendMessage('Create surface from index',
+                                          {'method': method, 'options': srf_options})
+
+                    filename = u'{}-{}.stl'.format(options.export_to_all, threshold_name)
+                    Publisher.sendMessage('Export surface to file', (filename, const.FILETYPE_STL))
+
+                    Publisher.sendMessage('Remove surfaces', [0])
+        except:
+            traceback.print_exc()
+        finally:
+            exit(0)
+
+
 def print_events(data):
     """
     Print pubsub messages
@@ -98,6 +98,8 @@ class Controller():
  
         Publisher.subscribe(self.SetBitmapSpacing, 'Set bitmap spacing')
  
+        Publisher.subscribe(self.OnSaveProject, 'Save project')
+
     def SetBitmapSpacing(self, pubsub_evt):
         proj = prj.Project()
         proj.spacing = pubsub_evt.data
@@ -335,6 +337,10 @@ class Controller():
         session.OpenProject(filepath)
         Publisher.sendMessage("Enable state project", True)
  
+    def OnSaveProject(self, pubsub_evt):
+        path = pubsub_evt.data
+        self.SaveProject(path)
+
     def SaveProject(self, path=None):
         Publisher.sendMessage('Begin busy cursor')
         session = ses.Session()
...	...	@@ -0,0 +1,3 @@
	1	+.git*
	2	+.python-version
	3	+Dockerfile
...	...
...	...	@@ -0,0 +1,31 @@
	1	+FROM ubuntu:16.04
	2	+
	3	+RUN apt-get update
	4	+RUN apt-get install -y \
	5	+ cython \
	6	+ python-concurrent.futures \
	7	+ python-gdcm \
	8	+ python-matplotlib \
	9	+ python-nibabel \
	10	+ python-numpy \
	11	+ python-pil \
	12	+ python-psutil \
	13	+ python-scipy \
	14	+ python-serial \
	15	+ python-skimage \
	16	+ python-vtk6 \
	17	+ python-vtkgdcm \
	18	+ python-wxgtk3.0 \
	19	+ xvfb # For a virtual X server.
	20	+
	21	+RUN apt-get install -y locales
	22	+RUN locale-gen en_US.UTF-8
	23	+ENV LANG en_US.UTF-8
	24	+ENV LANGUAGE en_US:en
	25	+ENV LC_ALL en_US.UTF-8
	26	+
	27	+WORKDIR /usr/local/app
	28	+
	29	+COPY . .
	30	+
	31	+RUN python setup.py build_ext --inplace
...	...
...	...	@@ -24,6 +24,7 @@ import optparse as op
24	24	import os
25	25	import sys
26	26	import shutil
	27	+import traceback
27	28
28	29	if sys.platform == 'win32':
29	30	import _winreg
...	...	@@ -245,6 +246,13 @@ def parse_comand_line():
245	246	parser.add_option("-i", "--import",
246	247	action="store",
247	248	dest="dicom_dir")
	249	+
	250	+ parser.add_option("-s", "--save",
	251	+ help="To save the project after an import.")
	252	+
	253	+ parser.add_option("-a", "--export-to-all",
	254	+ help="To open a project and export it to STL for all mask presets.")
	255	+
248	256	options, args = parser.parse_args()
249	257
250	258	# If debug argument...
...	...	@@ -256,23 +264,65 @@ def parse_comand_line():
256	264	if options.dicom_dir:
257	265	import_dir = options.dicom_dir
258	266	Publisher.sendMessage('Import directory', import_dir)
	267	+
	268	+ if options.save:
	269	+ Publisher.sendMessage('Save project', os.path.abspath(options.save))
	270	+ exit(0)
	271	+
	272	+ check_for_exporting(options)
	273	+
259	274	return True
260	275
261	276	# Check if there is a file path somewhere in what the user wrote
262	277	# In case there is, try opening as it was a inv3
263	278	else:
264		- i = len(args)
265		- while i:
266		- i -= 1
267		- file = args[i]
268		- if os.path.isfile(file):
269		- path = os.path.abspath(file)
270		- Publisher.sendMessage('Open project', path)
271		- i = 0
	279	+ for arg in reversed(args):
	280	+ if os.path.isfile(arg):
	281	+ path_ = os.path.abspath(arg)
	282	+ Publisher.sendMessage('Open project', path_)
	283	+
	284	+ check_for_exporting(options)
	285	+
272	286	return True
273	287	return False
274	288
275	289
	290	+def check_for_exporting(options):
	291	+ if options.export_to_all:
	292	+ try:
	293	+ method = {
	294	+ 'algorithm': 'Default',
	295	+ 'options': {},
	296	+ }
	297	+
	298	+ import invesalius.constants as const
	299	+ from invesalius.project import Project
	300	+
	301	+ for threshold_name, threshold_range in Project().presets.thresh_ct.iteritems():
	302	+ if isinstance(threshold_range[0], int):
	303	+ Publisher.sendMessage('Set threshold values', threshold_range)
	304	+
	305	+ srf_options = {
	306	+ 'index': 0,
	307	+ 'name': '',
	308	+ 'quality': _('Optimal *'),
	309	+ 'fill': False,
	310	+ 'keep_largest': False,
	311	+ 'overwrite': False,
	312	+ }
	313	+ Publisher.sendMessage('Create surface from index',
	314	+ {'method': method, 'options': srf_options})
	315	+
	316	+ filename = u'{}-{}.stl'.format(options.export_to_all, threshold_name)
	317	+ Publisher.sendMessage('Export surface to file', (filename, const.FILETYPE_STL))
	318	+
	319	+ Publisher.sendMessage('Remove surfaces', [0])
	320	+ except:
	321	+ traceback.print_exc()
	322	+ finally:
	323	+ exit(0)
	324	+
	325	+
276	326	def print_events(data):
277	327	"""
278	328	Print pubsub messages
...	...
...	...	@@ -98,6 +98,8 @@ class Controller():
98	98
99	99	Publisher.subscribe(self.SetBitmapSpacing, 'Set bitmap spacing')
100	100
	101	+ Publisher.subscribe(self.OnSaveProject, 'Save project')
	102	+
101	103	def SetBitmapSpacing(self, pubsub_evt):
102	104	proj = prj.Project()
103	105	proj.spacing = pubsub_evt.data
...	...	@@ -335,6 +337,10 @@ class Controller():
335	337	session.OpenProject(filepath)
336	338	Publisher.sendMessage("Enable state project", True)
337	339
	340	+ def OnSaveProject(self, pubsub_evt):
	341	+ path = pubsub_evt.data
	342	+ self.SaveProject(path)
	343	+
338	344	def SaveProject(self, path=None):
339	345	Publisher.sendMessage('Begin busy cursor')
340	346	session = ses.Session()
...	...