Example #1
0
    def save_outputs(self):

        # savestring_qt, ok = QInputDialog.getText(
        #     None,
        #     "Save",
        #     'Save output data? Yes/No/All with input data (y/n/a):',
        #     text="a"
        #     )

        # savestring = str(savestring_qt)

        #    if savestring in ['Y', 'y', 'a', 'A']:
        odp = self.output_datapath
        if not op.exists(odp):
            os.makedirs(odp)

        data = self.export()
        data['version'] = self.version  # qmisc.getVersionString()
        data['experiment_caption'] = self.experiment_caption
        data['lisa_operator_identifier'] = self.lisa_operator_identifier
#       data['organ_interactivity_counter'] = self.organ_interactivity_counter
        pth, filename = op.split(op.normpath(self.datapath))
        filename += "-" + self.experiment_caption
#        if savestring in ['a', 'A']:
# save renamed file too
        filepath = 'org-' + filename + '.' + self.save_filetype
        # rint filepath
        # rint 'op ', op
        filepath = op.join(odp, filepath)
        filepath = misc.suggest_filename(filepath)
        misc.obj_to_file(data, filepath, filetype=self.save_filetype)

        filepath = 'organ_last.' + self.save_filetype
        filepath = op.join(odp, filepath)
        # ilepath = misc.suggest_filename(filepath)
        misc.obj_to_file(data, filepath, filetype=self.save_filetype)
# save to mat

#        iparams = self.get_iparams()
        # filepath = 'organ_iparams.pklz'
        # filepath = op.join(odp, filepath)
        # misc.obj_to_file(iparams, filepath, filetype='pklz')

        # f savestring in ['a', 'A']:
        if False:
            # save renamed file too
            data['data3d'] = None
            filepath = 'organ_small-' + filename + '.pklz'
            filepath = op.join(odp, filepath)
            filepath = misc.suggest_filename(filepath)
            misc.obj_to_file(data, filepath, filetype='pklz')
Example #2
0
 def save_outputs_dcm_overlay(self):
     # TODO add
     logger.debug('save dcm')
     from PyQt4.QtCore import pyqtRemoveInputHook
     pyqtRemoveInputHook()
     # mport ipdb; ipdb.set_trace() # BREAKPOINT
     odp = self.output_datapath
     pth, filename = op.split(op.normpath(self.datapath))
     filename += "-" + self.experiment_caption
     # f savestring in ['ad']:
     #       save to DICOM
     filepath = 'dicom-' + filename
     filepath = os.path.join(odp, filepath)
     filepath = misc.suggest_filename(filepath)
     output_dicom_dir = filepath
     data = self.export()
     # mport ipdb; ipdb.set_trace()  # BREAKPOINT
     overlays = {
         3:
         (data['segmentation'] == self.output_label).astype(np.int8)
     }
     if self.dcmfilelist is not None:
         datawriter.saveOverlayToDicomCopy(
             self.dcmfilelist,
             output_dicom_dir, overlays,
             data['crinfo'], data['orig_shape'])
Example #3
0
    def test_suggest_filename(self):
        """
        Testing some files. Not testing recursion in filenames. It is situation
        if there exist file0, file1, file2 and input file is file
        """
        import misc
        filename = "mujsoubor"
        #import ipdb; ipdb.set_trace() # BREAKPOINT
        new_filename = misc.suggest_filename(filename, exists=True)
        self.assertTrue(new_filename == "mujsoubor2")

        filename = "mujsoubor112"
        new_filename = misc.suggest_filename(filename, exists=True)
        self.assertTrue(new_filename == "mujsoubor113")

        filename = "mujsoubor-2.txt"
        new_filename = misc.suggest_filename(filename, exists=True)
        self.assertTrue(new_filename == "mujsoubor-3.txt")

        filename = "mujsoubor-a24.txt"
        new_filename = misc.suggest_filename(filename, exists=False)
        self.assertTrue(new_filename == "mujsoubor-a24.txt")
Example #4
0
    def get_standard_ouptut_filename(self, filetype=None, suffix=''):
        """
        It can be settet filename, or filename end with suffix.
        """
        if filetype is None:
            filetype = self.save_filetype

        output_dir = self.output_datapath

        pth, filename = op.split(op.normpath(self.datapath))
        filename += "-" + self.experiment_caption
#        if savestring in ['a', 'A']:
# save renamed file too
        filename = '' + filename + suffix + '.' + filetype
        filepath = op.join(output_dir, filename)
        filepath = misc.suggest_filename(filepath)

        return filepath
Example #5
0
def save_outputs(args, oseg, qt_app):
    from PyQt4.QtGui import QInputDialog
    savestring_qt, ok = QInputDialog.getText(
        None,
        "Save",
        'Save output data? Yes/No/All+Dicom with input data (y/n/a/ad):',
        text="a"
    )
    savestring = str(savestring_qt)
    #import pdb; pdb.set_trace()
    #savestring = raw_input(
    #    'Save output data? Yes/No/All with input data (y/n/a): '
    #)
    if savestring in ['Y', 'y', 'a', 'A', 'ad']:
        if not os.path.exists(args["output_datapath"]):
            os.makedirs(args['output_datapath'])

        op = args['output_datapath']
# rename

        data = oseg.export()
        data['version'] = qmisc.getVersionString()
        data['experiment_caption'] = args['experiment_caption']
        data['lisa_operator_identifier'] = args['lisa_operator_identifier']
        #data['organ_segmentation_time'] = t1
        iparams = oseg.get_iparams()
        #import pdb; pdb.set_trace()
        pth, filename = os.path.split(os.path.normpath(args['datapath']))
        filename += "-" + args['experiment_caption']
        if savestring in ['a', 'A', 'ad']:
# save renamed file too
            filepath = 'ob-' + filename + '.pklz'
            filepath = os.path.join(op, filepath)
            filepath = misc.suggest_filename(filepath)
            misc.obj_to_file(data, filepath, filetype='pklz')

        filepath = 'organ.pklz'
        filepath = os.path.join(op, filepath)
        #filepath = misc.suggest_filename(filepath)
        misc.obj_to_file(data, filepath, filetype='pklz')

        filepath = 'organ_iparams.pklz'
        filepath = os.path.join(op, filepath)
        misc.obj_to_file(iparams, filepath, filetype='pklz')

        data['data3d'] = None
        filepath = 'organ_small-' + filename + '.pklz'
        filepath = os.path.join(op, filepath)
        filepath = misc.suggest_filename(filepath)
        misc.obj_to_file(data, filepath, filetype='pklz')
    #output = segmentation.vesselSegmentation(oseg.data3d,
    # oseg.orig_segmentation)
#    print "uf"

        if savestring in ['ad']:
            # save to DICOM
            filepath = 'dicom-' + filename
            filepath = os.path.join(op, filepath)
            filepath = misc.suggest_filename(filepath)
            output_dicom_dir = filepath
            #import ipdb; ipdb.set_trace()  # BREAKPOINT
            overlays = {
                3:
                (data['segmentation'] == args['output_label']).astype(np.int8)
            }
            saveOverlayToDicomCopy(oseg.metadata['dcmfilelist'],
                                   output_dicom_dir, overlays,
                                   data['crinfo'], data['orig_shape'])