Add command line options for saving and exporting (invesalius#85)

* Create option in app.py to import and then save the project

* Add command to import and export in STL to all available presets

* Create option to open InVesalius without gui

* Add option --export

* No-gui doing less work when creating surface

* Print on debug

* Fix missing session assignment in non-gui mode

* Add option to import every group of DICOM images

* Checking surface index exists in actors_dict before removing it

.dockerignore

@@ -0,0 +1,3 @@
+.git*
+.python-version
+Dockerfile

Dockerfile

@@ -0,0 +1,30 @@
+FROM ubuntu:16.04
+
+RUN apt-get update
+RUN apt-get install -y \
+    cython \
+    locales \
+    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
+
+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

app.py

@@ -24,6 +24,9 @@
 import os
 import sys
 import shutil
+import traceback
+
+import re
 
 if sys.platform == 'win32':
     import _winreg
@@ -218,7 +221,8 @@ def Startup(self):
         self.control = Controller(self.main)
 
         self.fc = wx.FutureCall(1, self.ShowMain)
-        wx.FutureCall(1, parse_comand_line)
+        options, args = parse_comand_line()
+        wx.FutureCall(1, use_cmd_optargs, options, args)
 
         # Check for updates
         from threading import Thread
@@ -244,6 +248,24 @@ def ShowMain(self):
         if self.fc.IsRunning():
             self.Raise()
 
+
+def non_gui_startup(options, args):
+    lang = 'en'
+    _ = i18n.InstallLanguage(lang)
+
+    from invesalius.control import Controller
+    from invesalius.project import Project
+
+    session = ses.Session()
+    if not session.ReadSession():
+        session.CreateItens()
+        session.SetLanguage(lang)
+        session.WriteSessionFile()
+
+    control = Controller(None)
+
+    use_cmd_optargs(options, args)
+
 # ------------------------------------------------------------------
 
 
@@ -262,39 +284,138 @@ def parse_comand_line():
                       action="store_true",
                       dest="debug")
 
+    parser.add_option('--no-gui',
+                      action='store_true',
+                      dest='no_gui')
+
     # -i or --import: import DICOM directory
     # chooses largest series
     parser.add_option("-i", "--import",
                       action="store",
                       dest="dicom_dir")
+
+    parser.add_option("--import-all",
+                      action="store")
+
+    parser.add_option("-s", "--save",
+                      help="Save the project after an import.")
+
+    parser.add_option("-t", "--threshold",
+                      help="Define the threshold for the export (e.g. 100-780).")
+
+    parser.add_option("-e", "--export",
+                      help="Export to STL.")
+
+    parser.add_option("-a", "--export-to-all",
+                      help="Export to STL for all mask presets.")
+
     options, args = parser.parse_args()
+    return options, args
+
 
+def use_cmd_optargs(options, args):
     # If debug argument...
     if options.debug:
         Publisher.subscribe(print_events, Publisher.ALL_TOPICS)
+        session = ses.Session()
         session.debug = 1
 
     # If import DICOM argument...
     if options.dicom_dir:
         import_dir = options.dicom_dir
-        Publisher.sendMessage('Import directory', import_dir)
+        Publisher.sendMessage('Import directory', {'directory': import_dir, 'gui': not options.no_gui})
+
+        if options.save:
+            Publisher.sendMessage('Save project', os.path.abspath(options.save))
+            exit(0)
+
+        check_for_export(options)
+
+        return True
+    elif options.import_all:
+        import invesalius.reader.dicom_reader as dcm
+        for patient in dcm.GetDicomGroups(options.import_all):
+            for group in patient.GetGroups():
+                Publisher.sendMessage('Import group', {'group': group, 'gui': not options.no_gui})
+                check_for_export(options, suffix=group.title, remove_surfaces=False)
+                Publisher.sendMessage('Remove masks', [0])
         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].decode(sys.stdin.encoding)
-            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.decode(sys.stdin.encoding))
+                Publisher.sendMessage('Open project', path_)
+
+                check_for_export(options)
                 return True
     return False
 
 
+def sanitize(text):
+    text = str(text).strip().replace(' ', '_')
+    return re.sub(r'(?u)[^-\w.]', '', text)
+
+
+def check_for_export(options, suffix='', remove_surfaces=False):
+    suffix = sanitize(suffix)
+
+    if options.export:
+        if not options.threshold:
+            print("Need option --threshold when using --export.")
+            exit(1)
+        threshold_range = tuple([int(n) for n in options.threshold.split(',')])
+
+        if suffix:
+            if options.export.endswith('.stl'):
+                path_ = '{}-{}.stl'.format(options.export[:-4], suffix)
+            else:
+                path_ = '{}-{}.stl'.format(options.export, suffix)
+        else:
+            path_ = options.export
+
+        export(path_, threshold_range, remove_surface=remove_surfaces)
+    elif options.export_to_all:
+        # noinspection PyBroadException
+        try:
+            from invesalius.project import Project
+
+            for threshold_name, threshold_range in Project().presets.thresh_ct.iteritems():
+                if isinstance(threshold_range[0], int):
+                    path_ = u'{}-{}-{}.stl'.format(options.export_to_all, suffix, threshold_name)
+                    export(path_, threshold_range, remove_surface=True)
+        except:
+            traceback.print_exc()
+        finally:
+            exit(0)
+
+
+def export(path_, threshold_range, remove_surface=False):
+    import invesalius.constants as const
+
+    Publisher.sendMessage('Set threshold values', threshold_range)
+
+    surface_options = {
+        'method': {
+            'algorithm': 'Default',
+            'options': {},
+        }, 'options': {
+            'index': 0,
+            'name': '',
+            'quality': _('Optimal *'),
+            'fill': False,
+            'keep_largest': False,
+            'overwrite': False,
+        }
+    }
+    Publisher.sendMessage('Create surface from index', surface_options)
+    Publisher.sendMessage('Export surface to file', (path_, const.FILETYPE_STL))
+    if remove_surface:
+        Publisher.sendMessage('Remove surfaces', [0])
+
+
 def print_events(data):
     """
     Print pubsub messages
@@ -305,8 +426,13 @@ def main():
     """
     Initialize InVesalius GUI
     """
-    application = InVesalius(0)
-    application.MainLoop()
+    options, args = parse_comand_line()
+
+    if options.no_gui:
+        non_gui_startup(options, args)
+    else:
+        application = InVesalius(0)
+        application.MainLoop()
 
 if __name__ == '__main__':
     #Is needed because of pyinstaller

invesalius/constants.py

@@ -694,19 +694,19 @@
             IR2: {1: 'REI'},
             IR3: {2: 'NAI'}}
 
-TIPS_IMG = [wx.ToolTip(_("Select left ear in image")),
-            wx.ToolTip(_("Select right ear in image")),
-            wx.ToolTip(_("Select nasion in image"))]
+TIPS_IMG = [_("Select left ear in image"),
+            _("Select right ear in image"),
+            _("Select nasion in image")]
 
 BTNS_TRK = {TR1: {3: _('LET')},
             TR2: {4: _('RET')},
             TR3: {5: _('NAT')},
             SET: {6: _('SET')}}
 
-TIPS_TRK = [wx.ToolTip(_("Select left ear with spatial tracker")),
-            wx.ToolTip(_("Select right ear with spatial tracker")),
-            wx.ToolTip(_("Select nasion with spatial tracker")),
-            wx.ToolTip(_("Show set coordinates in image"))]
+TIPS_TRK = [_("Select left ear with spatial tracker"),
+            _("Select right ear with spatial tracker"),
+            _("Select nasion with spatial tracker"),
+            _("Show set coordinates in image")]
 
 CAL_DIR = os.path.abspath(os.path.join(FILE_PATH, '..', 'navigation', 'mtc_files', 'CalibrationFiles'))
 MAR_DIR = os.path.abspath(os.path.join(FILE_PATH, '..', 'navigation', 'mtc_files', 'Markers'))

invesalius/control.py

@@ -68,6 +68,7 @@ def __init__(self, frame):
 
     def __bind_events(self):
         Publisher.subscribe(self.OnImportMedicalImages, 'Import directory')
+        Publisher.subscribe(self.OnImportGroup, 'Import group')
         Publisher.subscribe(self.OnShowDialogImportDirectory,
                                  'Show import directory dialog')
         Publisher.subscribe(self.OnShowDialogImportOtherFiles,
@@ -105,6 +106,8 @@ def __bind_events(self):
 
         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
@@ -329,6 +332,10 @@ def OpenProject(self, filepath):
         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()
@@ -442,18 +449,19 @@ def LoadImportPanel(self, patient_series):
     #----------- to import by command line ---------------------------------------------------
 
     def OnImportMedicalImages(self, pubsub_evt):
-        directory = pubsub_evt.data
-        self.ImportMedicalImages(directory)
+        directory = pubsub_evt.data['directory']
+        gui = pubsub_evt.data['gui']
+        self.ImportMedicalImages(directory, gui)
 
-    def ImportMedicalImages(self, directory):
+    def ImportMedicalImages(self, directory, gui=True):
         patients_groups = dcm.GetDicomGroups(directory)
         name = directory.rpartition('\\')[-1].split('.')
         print "patients: ", patients_groups
 
         if len(patients_groups):
             # OPTION 1: DICOM
             group = dcm.SelectLargerDicomGroup(patients_groups)
-            matrix, matrix_filename, dicom = self.OpenDicomGroup(group, 0, [0, 0], gui=True)
+            matrix, matrix_filename, dicom = self.OpenDicomGroup(group, 0, [0, 0], gui=gui)
             self.CreateDicomProject(dicom, matrix, matrix_filename)
         else:
             # OPTION 2: NIfTI, Analyze or PAR/REC
@@ -476,6 +484,18 @@ def ImportMedicalImages(self, directory):
         self.LoadProject()
         Publisher.sendMessage("Enable state project", True)
 
+    def OnImportGroup(self, pubsub_evt):
+        group = pubsub_evt.data['group']
+        gui = pubsub_evt.data['gui']
+        self.ImportGroup(group, gui)
+
+    def ImportGroup(self, group, gui=True):
+        matrix, matrix_filename, dicom = self.OpenDicomGroup(group, 0, [0, 0], gui=gui)
+        self.CreateDicomProject(dicom, matrix, matrix_filename)
+
+        self.LoadProject()
+        Publisher.sendMessage("Enable state project", True)
+
     #-------------------------------------------------------------------------------------
 
     def LoadProject(self):
@@ -785,7 +805,7 @@ def OpenDicomGroup(self, dicom_group, interval, file_range, gui=True):
         n_slices = len(filelist)
         resolution_percentage = utils.calculate_resizing_tofitmemory(int(sx), int(sy), n_slices, bits/8)
 
-        if resolution_percentage < 1.0:
+        if resolution_percentage < 1.0 and gui:
             re_dialog = dialog.ResizeImageDialog()
             re_dialog.SetValue(int(resolution_percentage*100))
             re_dialog_value = re_dialog.ShowModal()

invesalius/data/slice_.py

@@ -359,19 +359,22 @@ def __set_current_mask_threshold(self, evt_pubsub):
 
         # TODO: merge this code with apply_slice_buffer_to_mask
         b_mask = self.buffer_slices["AXIAL"].mask
-        n = self.buffer_slices["AXIAL"].index + 1
-        self.current_mask.matrix[n, 1:, 1:] = b_mask
-        self.current_mask.matrix[n, 0, 0] = 1
+        if b_mask is not None:
+            n = self.buffer_slices["AXIAL"].index + 1
+            self.current_mask.matrix[n, 1:, 1:] = b_mask
+            self.current_mask.matrix[n, 0, 0] = 1
 
         b_mask = self.buffer_slices["CORONAL"].mask
-        n = self.buffer_slices["CORONAL"].index + 1
-        self.current_mask.matrix[1:, n, 1:] = b_mask
-        self.current_mask.matrix[0, n, 0] = 1
+        if b_mask is not None:
+            n = self.buffer_slices["CORONAL"].index + 1
+            self.current_mask.matrix[1:, n, 1:] = b_mask
+            self.current_mask.matrix[0, n, 0] = 1
 
         b_mask = self.buffer_slices["SAGITAL"].mask
-        n = self.buffer_slices["SAGITAL"].index + 1
-        self.current_mask.matrix[1:, 1:, n] = b_mask
-        self.current_mask.matrix[0, 0, n] = 1
+        if b_mask is not None:
+            n = self.buffer_slices["SAGITAL"].index + 1
+            self.current_mask.matrix[1:, 1:, n] = b_mask
+            self.current_mask.matrix[0, 0, n] = 1
 
         if to_reload:
             Publisher.sendMessage('Reload actual slice')
@@ -888,7 +891,8 @@ def SetMaskThreshold(self, index, threshold_range, slice_number=None,
                     self.current_mask.matrix[n+1, 1:, 1:] = m
             else:
                 slice_ = self.buffer_slices[orientation].image
-                self.buffer_slices[orientation].mask = (255 * ((slice_ >= thresh_min) & (slice_ <= thresh_max))).astype('uint8')
+                if slice_ is not None:
+                    self.buffer_slices[orientation].mask = (255 * ((slice_ >= thresh_min) & (slice_ <= thresh_max))).astype('uint8')
 
             # Update viewer
             #Publisher.sendMessage('Update slice viewer')