class Summary(HasTraits):
summary_table = List(Data)
subject = Instance(Data)
view = QtView(
Item(
'summary_table',
editor=TableEditor(
editable=False,
selected='subject',
adapter=SummaryAdapter(),
# operations = [],
# images = [ op.abspath('green_ball.png'),
# op.abspath('red_ball.png'), ]
)),
resizable=True,
width=0.75,
height=0.75)
class EEGSensorApp(t.HasTraits):
sensor = t.Instance(EEGSensor)
filters = t.List(t.Instance(TimeDomainFilter))
sensor_operation_controller = t.Instance(SensorOperationController)
def _sensor_operation_controller_default(self):
return SensorOperationController(model=self.sensor)
sensor_timeseries_controller = t.Instance(SensorTimeseriesController)
def _sensor_timeseries_controller_default(self):
return SensorTimeseriesController(model=self.sensor,
filters=self.filters)
sensor_fft_controller = t.Instance(SensorFFTController)
def _sensor_fft_controller_default(self):
return SensorFFTController(model=self.sensor)
traits_view = QtView(
HGroup(
VGroup(Item('sensor_timeseries_controller', style='custom'),
show_border=True,
show_labels=False),
VGroup(Item('sensor_fft_controller', style='custom'),
Item('sensor_operation_controller', style='custom'),
show_border=True,
show_labels=False),
),
title="EEG Sensor Console",
icon=ImageResource('application'),
# style_sheet_path='dark_style_sheet.qss',
style_sheet=qdarkstyle.load_stylesheet(pyside=True),
resizable=True,
handler=AppHandler(),
)
class ProjectInfoUI(cmp.project.ProjectInfo):
"""Class that extends the :class:`ProjectInfo` with graphical components.
It supports graphically the setting of all processing properties / attributes
of an :class:`ProjectInfo` instance.
Attributes
-----------
creation_mode : traits.Enum
Mode for loading the dataset. Valid values are
'Load BIDS dataset', 'Install Datalad BIDS dataset'
install_datalad_dataset_via_ssh : traits.Bool
If set to True install the datalad dataset from a remote server
via ssh.(True by default)
ssh_user : traits.Str
Remote server username.
(Required if ``install_datalad_dataset_via_ssh`` is True)
ssh_pwd <traits.Password>
Remote server password.
(Required if ``install_datalad_dataset_via_ssh`` is True)
ssh_remote : traits.Str
Remote server IP or URL.
(Required if ``install_datalad_dataset_via_ssh`` is True)
datalad_dataset_path : traits.Directory
Path to the datalad dataset on the remote server.
(Required if ``install_datalad_dataset_via_ssh`` is True)
summary_view_button : traits.ui.Button
Button that shows the pipeline processing summary table
pipeline_processing_summary_view : traits.ui.VGroup
TraitsUI VGroup that contains ``Item('pipeline_processing_summary')``
dataset_view : traits.ui.View
TraitsUI View that shows a summary of project settings and
modality available for a given subject
traits_view : QtView
TraitsUI QtView that includes the View 'dataset_view'
create_view : traits.ui.View
Dialog view to create a BIDS Dataset
subject_view : traits.ui.View
Dialog view to select of subject
subject_session_view : traits.ui.View
Dialog view to select the subject session
dmri_bids_acq_view : traits.ui.View
Dialog view to select the diffusion acquisition model
anat_warning_view : traits.ui.View
View that displays a warning message regarding
the anatomical T1w data
anat_config_error_view : traits.ui.View
Error view that displays an error message regarding
the configuration of the anatomical pipeline
dmri_warning_view : traits.ui.View
View that displays a warning message regarding
the diffusion MRI data
dmri_config_error_view : traits.ui.View
View that displays an error message regarding
the configuration of the diffusion pipeline
fmri_warning_view : traits.ui.View
View that displays a warning message regarding
the functional MRI data
fmri_config_error_view : traits.ui.View
View that displays an error message regarding
the configuration of the fMRI pipeline
open_view : traits.ui.View
Dialog view to load a BIDS Dataset
anat_select_config_to_load : traits.ui.View
Dialog view to load the configuration file of the anatomical pipeline
diffusion_imaging_model_select_view : traits.ui.View
Dialog view to select the diffusion acquisition model
dmri_select_config_to_load : traits.ui.View
Dialog view to load the configuration file of the diffusion MRI pipeline
fmri_select_config_to_load : traits.ui.View
Dialog view to load the configuration file of the fMRI pipeline
"""
creation_mode = Enum("Load BIDS dataset", "Install Datalad BIDS dataset")
install_datalad_dataset_via_ssh = Bool(True)
ssh_user = String("remote_username")
ssh_pwd = Password("")
ssh_remote = String("IP address/ Machine name")
datalad_dataset_path = Directory(
"/shared/path/to/existing/datalad/dataset")
anat_runs = List()
anat_run = Enum(values="anat_runs")
dmri_runs = List()
dmri_run = Enum(values="dmri_runs")
fmri_runs = List()
fmri_run = Enum(values="fmri_runs")
summary_view_button = Button("Pipeline processing summary")
pipeline_processing_summary_view = VGroup(
Item("pipeline_processing_summary"))
dataset_view = VGroup(
VGroup(
HGroup(
Item(
"base_directory",
width=-0.3,
style="readonly",
label="",
resizable=True,
),
Item(
"number_of_subjects",
width=-0.3,
style="readonly",
label="Number of participants",
resizable=True,
),
"summary_view_button",
),
label="BIDS Dataset",
),
spring,
HGroup(
Group(
Item("subject",
style="simple",
show_label=True,
resizable=True)),
Group(
Item("subject_session",
style="simple",
label="Session",
resizable=True),
visible_when='subject_session!=""',
),
springy=True,
),
spring,
Group(
Item("t1_available", style="readonly", label="T1", resizable=True),
HGroup(
Item(
"dmri_available",
style="readonly",
label="Diffusion",
resizable=True,
),
Item(
"diffusion_imaging_model",
label="Model",
resizable=True,
enabled_when="dmri_available",
),
),
Item("fmri_available",
style="readonly",
label="BOLD",
resizable=True),
label="Modalities",
),
spring,
Group(
Item(
"anat_last_date_processed",
label="Anatomical pipeline",
style="readonly",
resizable=True,
enabled_when="t1_available",
),
Item(
"dmri_last_date_processed",
label="Diffusion pipeline",
style="readonly",
resizable=True,
enabled_when="dmri_available",
),
Item(
"fmri_last_date_processed",
label="fMRI pipeline",
style="readonly",
resizable=True,
enabled_when="fmri_available",
),
label="Last date processed",
),
spring,
Group(Item("number_of_cores", resizable=True),
label="Processing configuration"),
"550",
spring,
springy=True,
)
traits_view = QtView(Include("dataset_view"))
create_view = View(
Item("creation_mode", style="custom"),
Group(
Group(
Item("base_directory", label="BIDS Dataset"),
visible_when='creation_mode=="Load BIDS dataset"',
),
Group(
Item("install_datalad_dataset_via_ssh"),
visible_when='creation_mode=="Install Datalad/BIDS dataset"',
),
Group(
Item(
"ssh_remote",
label="Remote ssh server",
visible_when="install_datalad_dataset_via_ssh",
),
Item(
"ssh_user",
label="Remote username",
visible_when="install_datalad_dataset_via_ssh",
),
Item(
"ssh_pwd",
label="Remote password",
visible_when="install_datalad_dataset_via_ssh",
),
Item(
"datalad_dataset_path",
label="Datalad/BIDS Dataset Path/URL to be installed",
),
Item("base_directory", label="Installation directory"),
visible_when='creation_mode=="Install Datalad/BIDS dataset"',
),
),
kind="livemodal",
title="Data creation: BIDS dataset selection",
# style_sheet=style_sheet,
width=modal_width,
buttons=["OK", "Cancel"],
)
subject_view = View(
Group(Item("subject", label="Selected Subject")),
kind="modal",
title="Subject and session selection",
# style_sheet=style_sheet,
width=modal_width,
buttons=["OK", "Cancel"],
)
subject_session_view = View(
Group(
Item("subject", style="readonly", label="Selected Subject"),
Item("subject_session", label="Selected Session"),
),
kind="modal",
title="Session selection",
# style_sheet=style_sheet,
width=modal_width,
buttons=["OK", "Cancel"],
)
dmri_bids_acq_view = View(
Group(Item("dmri_bids_acq", label="Selected model"), ),
kind="modal",
title="Selection of diffusion acquisition model",
# style_sheet=style_sheet,
width=modal_width,
buttons=["OK", "Cancel"],
)
anat_warning_view = View(
Group(Item("anat_warning_msg", style="readonly", show_label=False), ),
title="Warning : Anatomical T1w data",
kind="modal",
width=modal_width,
# style_sheet=style_sheet,
buttons=["OK", "Cancel"],
)
anat_config_error_view = View(
Group(
Item("anat_config_error_msg", style="readonly",
show_label=False), ),
title="Error",
kind="modal",
width=modal_width,
# style_sheet=style_sheet,
buttons=["OK", "Cancel"],
)
dmri_warning_view = View(
Group(Item("dmri_warning_msg", style="readonly", show_label=False), ),
title="Warning : Diffusion MRI data",
kind="modal",
width=modal_width,
# style_sheet=style_sheet,
buttons=["OK", "Cancel"],
)
dmri_config_error_view = View(
Group(
Item("dmri_config_error_msg", style="readonly",
show_label=False), ),
title="Error",
kind="modal",
width=modal_width,
# style_sheet=style_sheet,
buttons=["OK", "Cancel"],
)
fmri_warning_view = View(
Group(Item("fmri_warning_msg", style="readonly", show_label=False), ),
title="Warning : fMRI data",
kind="modal",
width=modal_width,
# style_sheet=style_sheet,
buttons=["OK", "Cancel"],
)
fmri_config_error_view = View(
Group(
Item("fmri_config_error_msg", style="readonly",
show_label=False), ),
title="Error",
kind="modal",
width=modal_width,
# style_sheet=style_sheet,
buttons=["OK", "Cancel"],
)
open_view = View(
Item("creation_mode", label="Mode"),
Group(
Item("install_datalad_dataset_via_ssh"),
Item(
"ssh_remote",
label="Remote ssh server",
visible_when="install_datalad_dataset_via_ssh",
),
Item(
"ssh_user",
label="Remote username",
visible_when="install_datalad_dataset_via_ssh",
),
Item(
"ssh_pwd",
label="Remote password",
visible_when="install_datalad_dataset_via_ssh",
),
Item(
"datalad_dataset_path",
label="Datalad/BIDS Dataset Path/URL to be installed",
),
Item("base_directory", label="Installation directory"),
visible_when='creation_mode=="Install Datalad BIDS dataset"',
),
Group(
Item("base_directory", label="BIDS Dataset"),
visible_when='creation_mode=="Load BIDS dataset"',
),
kind="livemodal",
title="BIDS Dataset Creation/Loading",
# style_sheet=style_sheet,
width=600,
height=250,
buttons=["OK", "Cancel"],
)
anat_select_config_to_load = View(
Group(
Item("anat_config_to_load_msg", style="readonly",
show_label=False),
Item(
"anat_config_to_load",
style="custom",
editor=EnumEditor(name="anat_available_config"),
show_label=False,
),
),
title="Select configuration for anatomical pipeline",
kind="modal",
width=modal_width,
# style_sheet=style_sheet,
buttons=["OK", "Cancel"],
)
anat_custom_map_view = View(
Group(
Item(
"anat_custom_last_stage",
editor=EnumEditor(name="anat_stage_names"),
style="custom",
show_label=False,
), ),
title="Select until which stage to process the anatomical pipeline.",
kind="modal",
width=modal_width,
# style_sheet=style_sheet,
buttons=["OK", "Cancel"],
)
diffusion_imaging_model_select_view = View(
Group(Item("diffusion_imaging_model",
label="Diffusion MRI modality"), ),
title="Please select diffusion MRI modality",
kind="modal",
width=modal_width,
buttons=["OK", "Cancel"],
)
dmri_select_config_to_load = View(
Group(
Item("dmri_config_to_load_msg", style="readonly",
show_label=False), ),
Item(
"dmri_config_to_load",
style="custom",
editor=EnumEditor(name="dmri_available_config"),
show_label=False,
),
title="Select configuration for diffusion pipeline",
kind="modal",
width=modal_width,
# style_sheet=style_sheet,
buttons=["OK", "Cancel"],
)
dmri_custom_map_view = View(
Group(
Item(
"dmri_custom_last_stage",
editor=EnumEditor(name="dmri_stage_names"),
style="custom",
show_label=False,
), ),
title="Select until which stage to process the diffusion pipeline.",
kind="modal",
width=modal_width,
# style_sheet=style_sheet,
buttons=["OK", "Cancel"],
)
fmri_select_config_to_load = View(
Group(
Item("fmri_config_to_load_msg", style="readonly",
show_label=False), ),
Item(
"fmri_config_to_load",
style="custom",
editor=EnumEditor(name="fmri_available_config"),
show_label=False,
),
title="Select configuration for fMRI pipeline",
kind="modal",
width=modal_width,
# style_sheet=style_sheet,
buttons=["OK", "Cancel"],
)
fmri_custom_map_view = View(
Group(
Item(
"fmri_custom_last_stage",
editor=EnumEditor(name="fmri_stage_names"),
style="custom",
show_label=False,
), ),
title="Select until which stage to process the fMRI pipeline.",
kind="modal",
width=modal_width,
# style_sheet=style_sheet,
buttons=["OK", "Cancel"],
)
def _summary_view_button_fired(self):
self.configure_traits(view="pipeline_processing_summary_view")
class QualityInspectorWindow(HasTraits):
"""Class that defines the Quality Inspector Window.
Attributes
----------
project_info : cmp.project.ProjectInfo
Instance of :class:`CMP_Project_Info` that represents the processing project
anat_pipeline : Instance(HasTraits)
Instance of anatomical MRI pipeline
dmri_pipeline : Instance(HasTraits)
Instance of diffusion MRI pipeline
fmri_pipeline : Instance(HasTraits)
Instance of functional MRI pipeline
anat_inputs_checked : traits.Bool
Indicates if inputs of anatomical pipeline are available
(Default: False)
dmri_inputs_checked : traits.Bool
Indicates if inputs of diffusion pipeline are available
(Default: False)
fmri_inputs_checked : traits.Bool
Indicates if inputs of functional pipeline are available
(Default: False)
output_anat_available : traits.Bool
Indicates if outputs of anatomical pipeline are available
(Default: False)
output_dmri_available : traits.Bool
Indicates if outputs of diffusion pipeline are available
(Default: False)
output_fmri_available : traits.Bool
Indicates if outputs of functional pipeline are available
(Default: False)
traits_view : QtView
TraitsUI QtView that describes the content of the window
"""
project_info = Instance(cmp.project.ProjectInfo)
anat_pipeline = Instance(HasTraits)
dmri_pipeline = Instance(HasTraits)
fmri_pipeline = Instance(HasTraits)
anat_inputs_checked = Bool(False)
dmri_inputs_checked = Bool(False)
fmri_inputs_checked = Bool(False)
output_anat_available = Bool(False)
output_dmri_available = Bool(False)
output_fmri_available = Bool(False)
traits_view = QtView(
Group(
# Group(
# # Include('dataset_view'),label='Data manager',springy=True
# Item('project_info',style='custom',show_label=False),label='Data manager',springy=True, dock='tab'
# ),
Group(
Item("anat_pipeline", style="custom", show_label=False),
visible_when="output_anat_available",
label="Anatomical pipeline",
dock="tab",
),
Group(
Item(
"dmri_pipeline",
style="custom",
show_label=False,
visible_when="output_dmri_available",
),
label="Diffusion pipeline",
dock="tab",
),
Group(
Item(
"fmri_pipeline",
style="custom",
show_label=False,
visible_when="output_fmri_available",
),
label="fMRI pipeline",
dock="tab",
),
orientation="horizontal",
layout="tabbed",
springy=True,
enabled_when="output_anat_available",
),
title="Connectome Mapper 3 Inspector",
menubar=MenuBar(
Menu(
ActionGroup(Action(name="Quit", action="_on_close"), ),
name="File",
), ),
handler=cmp.bidsappmanager.gui.handlers.ConfigQualityWindowHandler(),
style_sheet=style_sheet,
width=0.5,
height=0.8,
resizable=True, # scrollable=True,
# icon=get_icon("qualitycontrol.png")
)
error_msg = Str("")
error_view = View(
Group(Item("error_msg", style="readonly", show_label=False), ),
title="Error",
kind="modal",
# style_sheet=style_sheet,
buttons=["OK"],
)
def __init__(
self,
project_info=None,
anat_inputs_checked=False,
dmri_inputs_checked=False,
fmri_inputs_checked=False,
):
"""Constructor of an :class:``PipelineConfiguratorWindow`` instance.
Parameters
----------
project_info : cmp.project.ProjectInfo
:class:`CMP_Project_Info` object (Default: None)
anat_inputs_checked : traits.Bool
Boolean that indicates if anatomical pipeline inputs are available
(Default: False)
dmri_inputs_checked = : traits.Bool
Boolean that indicates if diffusion pipeline inputs are available
(Default: False)
fmri_inputs_checked : traits.Bool
Boolean that indicates if functional pipeline inputs are available
(Default: False)
"""
print("> Initialize window...")
self.project_info = project_info
self.anat_inputs_checked = anat_inputs_checked
self.dmri_inputs_checked = dmri_inputs_checked
self.fmri_inputs_checked = fmri_inputs_checked
aborded = self.select_subject()
if aborded:
raise Exception(
BColors.FAIL +
" .. ABORDED: The quality control window will not be displayed."
+
"Selection of subject/session was cancelled at initialization."
+ BColors.ENDC)
def select_subject(self):
"""Function to select the subject and session for which to inspect outputs."""
print(
"> Selection of subject (and session) for which to inspect outputs"
)
valid_selected_subject = False
select = True
aborded = False
while not valid_selected_subject and not aborded:
# Select subject from BIDS dataset
np_res = self.project_info.configure_traits(view="subject_view")
if not np_res:
aborded = True
break
print(" .. INFO: Selected subject: {}".format(
self.project_info.subject))
# Select session if any
bids_layout = BIDSLayout(self.project_info.base_directory)
subject = self.project_info.subject.split("-")[1]
sessions = bids_layout.get(target="session",
return_type="id",
subject=subject)
if len(sessions) > 0:
print(" .. INFO: Input dataset has sessions")
print(sessions)
self.project_info.subject_sessions = []
for ses in sessions:
self.project_info.subject_sessions.append("ses-" +
str(ses))
np_res = self.project_info.configure_traits(
view="subject_session_view")
if not np_res:
aborded = True
break
self.project_info.anat_config_file = os.path.join(
self.project_info.base_directory,
"derivatives",
__cmp_directory__,
"{}".format(self.project_info.subject),
"{}".format(self.project_info.subject_session),
"{}_{}_anatomical_config.json".format(
self.project_info.subject,
self.project_info.subject_session),
)
if os.access(self.project_info.anat_config_file, os.F_OK):
print("> Initialize anatomical pipeline")
self.anat_pipeline = project.init_anat_project(
self.project_info, False)
else:
self.anat_pipeline = None
if self.dmri_inputs_checked:
self.project_info.dmri_config_file = os.path.join(
self.project_info.base_directory,
"derivatives",
__cmp_directory__,
"{}".format(self.project_info.subject),
"{}".format(self.project_info.subject_session),
"{}_{}_diffusion_config.json".format(
self.project_info.subject,
self.project_info.subject_session),
)
if os.access(self.project_info.dmri_config_file, os.F_OK):
print("> Initialize diffusion pipeline")
(
dmri_valid_inputs,
self.dmri_pipeline,
) = project.init_dmri_project(self.project_info,
bids_layout, False)
else:
self.dmri_pipeline = None
# self.dmri_pipeline.subject = self.project_info.subject
# self.dmri_pipeline.global_conf.subject = self.project_info.subject
if self.fmri_inputs_checked:
self.project_info.fmri_config_file = os.path.join(
self.project_info.base_directory,
"derivatives",
__cmp_directory__,
"{}".format(self.project_info.subject),
"{}".format(self.project_info.subject_session),
"{}_{}_fMRI_config.json".format(
self.project_info.subject,
self.project_info.subject_session),
)
if os.access(self.project_info.fmri_config_file, os.F_OK):
print("> Initialize fMRI pipeline")
(
fmri_valid_inputs,
self.fmri_pipeline,
) = project.init_fmri_project(self.project_info,
bids_layout, False)
else:
self.fmri_pipeline = None
# self.fmri_pipeline.subject = self.project_info.subject
# self.fmri_pipeline.global_conf.subject = self.project_info.subject
# self.anat_pipeline.global_conf.subject_session = self.project_info.subject_session
# if self.dmri_pipeline is not None:
# self.dmri_pipeline.global_conf.subject_session = self.project_info.subject_session
#
# if self.fmri_pipeline is not None:
# self.fmri_pipeline.global_conf.subject_session = self.project_info.subject_session
print(" .. INFO: Selected session %s" %
self.project_info.subject_session)
if self.anat_pipeline is not None:
self.anat_pipeline.stages[
"Segmentation"].config.freesurfer_subject_id = os.path.join(
self.project_info.base_directory,
"derivatives",
__freesurfer_directory__,
"{}_{}".format(self.project_info.subject,
self.project_info.subject_session),
)
else:
print(" .. INFO: No session detected")
self.project_info.anat_config_file = os.path.join(
self.project_info.base_directory,
"derivatives",
__cmp_directory__,
"{}".format(self.project_info.subject),
"{}_anatomical_config.json".format(
self.project_info.subject),
)
if os.access(self.project_info.anat_config_file, os.F_OK):
self.anat_pipeline = project.init_anat_project(
self.project_info, False)
else:
self.anat_pipeline = None
if self.dmri_inputs_checked:
self.project_info.dmri_config_file = os.path.join(
self.project_info.base_directory,
"derivatives",
__cmp_directory__,
"{}".format(self.project_info.subject),
"{}_diffusion_config.json".format(
self.project_info.subject),
)
if os.access(self.project_info.dmri_config_file, os.F_OK):
(
dmri_valid_inputs,
self.dmri_pipeline,
) = project.init_dmri_project(self.project_info,
bids_layout, False)
else:
self.dmri_pipeline = None
# self.dmri_pipeline.subject = self.project_info.subject
# self.dmri_pipeline.global_conf.subject = self.project_info.subject
if self.fmri_inputs_checked:
self.project_info.fmri_config_file = os.path.join(
self.project_info.base_directory,
"derivatives",
__cmp_directory__,
"{}".format(self.project_info.subject),
"{}_fMRI_config.json".format(
self.project_info.subject),
)
if os.access(self.project_info.fmri_config_file, os.F_OK):
(
fmri_valid_inputs,
self.fmri_pipeline,
) = project.init_fmri_project(self.project_info,
bids_layout, False)
else:
self.fmri_pipeline = None
# self.fmri_pipeline.subject = self.project_info.subject
# self.fmri_pipeline.global_conf.subject = self.project_info.subject
# self.anat_pipeline.global_conf.subject_session = ''
if self.anat_pipeline is not None:
self.anat_pipeline.stages[
"Segmentation"].config.freesurfer_subjects_dir = os.path.join(
self.project_info.base_directory,
"derivatives",
__freesurfer_directory__,
"{}".format(self.project_info.subject),
)
if self.anat_pipeline is not None:
print("> Anatomical pipeline output inspection")
self.anat_pipeline.view_mode = "inspect_outputs_view"
for stage in list(self.anat_pipeline.stages.values()):
print(" ... Inspect stage {}".format(stage))
stage.define_inspect_outputs()
# print('Stage {}: {}'.format(stage.stage_dir, stage.inspect_outputs))
if (len(stage.inspect_outputs) >
0) and (stage.inspect_outputs[0] !=
"Outputs not available"):
self.output_anat_available = True
if self.dmri_pipeline is not None:
print("> Diffusion pipeline output inspection")
self.dmri_pipeline.view_mode = "inspect_outputs_view"
for stage in list(self.dmri_pipeline.stages.values()):
print(" ... Inspect stage {}".format(stage))
stage.define_inspect_outputs()
# print('Stage {}: {}'.format(stage.stage_dir, stage.inspect_outputs))
if (len(stage.inspect_outputs) >
0) and (stage.inspect_outputs[0] !=
"Outputs not available"):
self.output_dmri_available = True
if self.fmri_pipeline is not None:
print("> fMRI pipeline output inspection")
self.fmri_pipeline.view_mode = "inspect_outputs_view"
for stage in list(self.fmri_pipeline.stages.values()):
print(" ... Inspect stage {}".format(stage))
stage.define_inspect_outputs()
# print('Stage {}: {}'.format(stage.stage_dir, stage.inspect_outputs))
if (len(stage.inspect_outputs) >
0) and (stage.inspect_outputs[0] !=
"Outputs not available"):
self.output_fmri_available = True
print_blue(" .. Anatomical output(s) available : %s" %
self.output_anat_available)
print_blue(" .. Diffusion output(s) available : %s" %
self.output_dmri_available)
print_blue(" .. fMRI output(s) available : %s" %
self.output_fmri_available)
if (self.output_anat_available or self.output_dmri_available
or self.output_fmri_available):
valid_selected_subject = True
else:
self.error_msg = (
" .. ERROR: No output available! " +
"Please select another subject (and session if any)!")
print_error(self.error_msg)
select = error(message=self.error_msg,
title="Error",
buttons=["OK", "Cancel"])
aborded = not select
return aborded
def update_diffusion_imaging_model(self, new):
"""Function called when ``diffusion_imaging_model`` is updated."""
self.dmri_pipeline.diffusion_imaging_model = new
class DiffusionPipelineUI(DiffusionPipeline):
"""Class that extends the :class:`~cmp.pipelines.diffusion.diffusion.DiffusionPipeline` with graphical components.
Attributes
----------
preprocessing : traits.ui.Button
Button to open the window for configuration or quality inspection
of the preprocessing stage depending on the ``view_mode``
registration : traits.ui.Button
Button to open the window for configuration or quality inspection
of the registration stage depending on the ``view_mode``
diffusion : traits.ui.Button
Button to open the window for configuration or quality inspection
of the diffusion reconstruction and tractography stage depending
on the ``view_mode``
connectome : traits.ui.Button
Button to open the window for configuration or quality inspection
of the connectome stage depending on the ``view_mode``
view_mode : ['config_view', 'inspect_outputs_view']
Variable used to control the display of either (1) the configuration
or (2) the quality inspection of stage of the pipeline
pipeline_group : traitsUI panel
Panel defining the layout of the buttons of the stages with corresponding images
traits_view : QtView
QtView that includes the ``pipeline_group`` panel
See also
---------
cmp.pipelines.diffusion.diffusion.DiffusionPipeline
"""
view_mode = Enum('config_view', ['config_view', 'inspect_outputs_view'])
preprocessing = Button('Preprocessing')
# preprocessing.setIcon(QIcon(QPixmap("preprocessing.png")))
diffusion = Button('Diffusion')
# diffusion.setIcon(QIcon(QPixmap("diffusion.png")))
registration = Button('Registration')
# registration.setIcon(QIcon(QPixmap("registration.png")))
connectome = Button('Connectome')
# connectome.setIcon(QIcon(QPixmap("connectome.png")))
pipeline_group = VGroup(
HGroup(spring,
UItem('preprocessing',
style='custom',
width=222,
height=129,
resizable=False,
style_sheet=return_button_style_sheet(
ImageResource('preprocessing').absolute_path)),
spring,
show_labels=False,
label="",
padding=0),
HGroup(spring,
UItem('registration',
style='custom',
width=222,
height=129,
resizable=False,
style_sheet=return_button_style_sheet(
ImageResource('registration').absolute_path)),
spring,
show_labels=False,
label="",
padding=0),
HGroup(spring,
UItem('diffusion',
style='custom',
width=222,
height=244,
resizable=False,
style_sheet=return_button_style_sheet(
ImageResource('diffusion').absolute_path)),
spring,
show_labels=False,
label="",
padding=0),
HGroup(spring,
UItem('connectome',
style='custom',
width=222,
height=129,
resizable=False,
style_sheet=return_button_style_sheet(
ImageResource('connectome').absolute_path)),
spring,
show_labels=False,
label="",
padding=0),
padding=0,
# layout='split',
# springy=True
)
traits_view = QtView(Include('pipeline_group'))
def __init__(self, project_info):
"""Constructor of the DiffusionPipelineUI class.
Parameters
-----------
project_info : cmp.project.CMP_Project_Info
CMP_Project_Info object that stores general information
such as the BIDS root and output directories (see
:class_`cmp.project.CMP_Project_Info` for more details)
See Also
---------
cmp.pipelines.diffusion.DiffusionPipeline.__init__
"""
DiffusionPipeline.__init__(self, project_info)
self.stages = {
'Preprocessing':
PreprocessingStageUI(bids_dir=project_info.base_directory,
output_dir=project_info.output_directory),
'Registration':
RegistrationStageUI(
pipeline_mode="Diffusion",
fs_subjects_dir=project_info.freesurfer_subjects_dir,
fs_subject_id=os.path.basename(
project_info.freesurfer_subject_id),
bids_dir=project_info.base_directory,
output_dir=self.output_directory),
'Diffusion':
DiffusionStageUI(bids_dir=project_info.base_directory,
output_dir=project_info.output_directory),
'Connectome':
ConnectomeStageUI(bids_dir=project_info.base_directory,
output_dir=project_info.output_directory)
}
for stage in list(self.stages.keys()):
if project_info.subject_session != '':
self.stages[stage].stage_dir = os.path.join(
self.base_directory, "derivatives", 'nipype', self.subject,
project_info.subject_session, self.pipeline_name,
self.stages[stage].name)
else:
self.stages[stage].stage_dir = os.path.join(
self.base_directory, "derivatives", 'nipype', self.subject,
self.pipeline_name, self.stages[stage].name)
def _preprocessing_fired(self, info):
"""Method that displays the window for the preprocessing stage.
The window changed accordingly to the value of ``view_mode`` to be
in configuration or quality inspection mode.
Parameters
-----------
info : traits.ui.Button
The preprocessing button object
"""
self.stages['Preprocessing'].configure_traits(view=self.view_mode)
def _diffusion_fired(self, info):
"""Method that displays the window for the diffusion stage.
The window changed accordingly to the value of ``view_mode`` to be
in configuration or quality inspection mode.
Parameters
-----------
info : traits.ui.Button
The diffusion button object
"""
self.stages['Diffusion'].configure_traits(view=self.view_mode)
def _registration_fired(self, info):
"""Method that displays the window for the registration stage.
The window changed accordingly to the value of ``view_mode`` to be
in configuration or quality inspection mode.
Parameters
-----------
info : traits.ui.Button
The registration button object
"""
self.stages['Registration'].configure_traits(view=self.view_mode)
def _connectome_fired(self, info):
"""Method that displays the window for the connectome stage.
The window changed accordingly to the value of ``view_mode`` to be
in configuration or quality inspection mode.
Parameters
-----------
info : traits.ui.Button
The connectome button object
"""
self.stages['Connectome'].configure_traits(view=self.view_mode)
def check_input(self, layout, gui=True):
"""Method that checks if inputs of the diffusion pipeline are available in the datasets.
Parameters
-----------
layout : bids.BIDSLayout
BIDSLayout object used to query
gui : bool
If True, display message in GUI
Returns
-------
valid_inputs : bool
True in all inputs of the anatomical pipeline are available
"""
print('**** Check Inputs ****')
diffusion_available = False
bvecs_available = False
bvals_available = False
valid_inputs = False
if self.global_conf.subject_session == '':
subject = self.subject
else:
subject = "_".join(
(self.subject, self.global_conf.subject_session))
dwi_file = os.path.join(self.subject_directory, 'dwi',
subject + '_dwi.nii.gz')
bval_file = os.path.join(self.subject_directory, 'dwi',
subject + '_dwi.bval')
bvec_file = os.path.join(self.subject_directory, 'dwi',
subject + '_dwi.bvec')
subjid = self.subject.split("-")[1]
try:
layout = BIDSLayout(self.base_directory)
print("Valid BIDS dataset with %s subjects" %
len(layout.get_subjects()))
for subj in layout.get_subjects():
self.global_conf.subjects.append('sub-' + str(subj))
# self.global_conf.subjects = ['sub-'+str(subj) for subj in layout.get_subjects()]
# self.global_conf.modalities = [
# str(mod) for mod in layout.get_modalities()]
# mods = layout.get_modalities()
types = layout.get_modalities()
# print "Available modalities :"
# for mod in mods:
# print "-%s" % mod
if self.global_conf.subject_session == '':
files = layout.get(subject=subjid,
suffix='dwi',
extensions='.nii.gz')
if len(files) > 0:
dwi_file = os.path.join(files[0].dirname,
files[0].filename)
print(dwi_file)
else:
error(message="Diffusion image not found for subject %s." %
subjid,
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
return
files = layout.get(subject=subjid,
suffix='dwi',
extensions='.bval')
if len(files) > 0:
bval_file = os.path.join(files[0].dirname,
files[0].filename)
print(bval_file)
else:
error(
message="Diffusion bval image not found for subject %s."
% subjid,
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
return
files = layout.get(subject=subjid,
suffix='dwi',
extensions='.bvec')
if len(files) > 0:
bvec_file = os.path.join(files[0].dirname,
files[0].filename)
print(bvec_file)
else:
error(
message="Diffusion bvec image not found for subject %s."
% subjid,
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
return
else:
sessid = self.global_conf.subject_session.split("-")[1]
files = layout.get(subject=subjid,
suffix='dwi',
extensions='.nii.gz',
session=sessid)
if len(files) > 0:
dwi_file = os.path.join(files[0].dirname,
files[0].filename)
print(dwi_file)
else:
error(
message=
"Diffusion image not found for subject %s, session %s."
% (subjid, self.global_conf.subject_session),
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
return
files = layout.get(subject=subjid,
suffix='dwi',
extensions='.bval',
session=sessid)
if len(files) > 0:
bval_file = os.path.join(files[0].dirname,
files[0].filename)
print(bval_file)
else:
error(
message=
"Diffusion bval image not found for subject %s, session %s."
% (subjid, self.global_conf.subject_session),
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
return
files = layout.get(subject=subjid,
suffix='dwi',
extensions='.bvec',
session=sessid)
if len(files) > 0:
bvec_file = os.path.join(files[0].dirname,
files[0].filename)
print(bvec_file)
else:
error(
message=
"Diffusion bvec image not found for subject %s, session %s."
% (subjid, self.global_conf.subject_session),
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
return
print("Looking for....")
print("dwi_file : %s" % dwi_file)
print("bvecs_file : %s" % bvec_file)
print("bvals_file : %s" % bval_file)
if os.path.isfile(dwi_file):
print("DWI available")
diffusion_available = True
except Exception:
error(
message=
"Invalid BIDS dataset. Please see documentation for more details.",
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
return
if os.path.isfile(bval_file):
bvals_available = True
if os.path.isfile(bvec_file):
bvecs_available = True
if diffusion_available:
if bvals_available and bvecs_available:
self.stages[
'Diffusion'].config.diffusion_imaging_model_choices = self.diffusion_imaging_model
# Copy diffusion data to derivatives / cmp / subject / dwi
if self.global_conf.subject_session == '':
out_dwi_file = os.path.join(self.derivatives_directory,
'cmp', self.subject, 'dwi',
subject + '_dwi.nii.gz')
out_bval_file = os.path.join(self.derivatives_directory,
'cmp', self.subject, 'dwi',
subject + '_dwi.bval')
out_bvec_file = os.path.join(self.derivatives_directory,
'cmp', self.subject, 'dwi',
subject + '_dwi.bvec')
else:
out_dwi_file = os.path.join(
self.derivatives_directory, 'cmp', self.subject,
self.global_conf.subject_session, 'dwi',
subject + '_dwi.nii.gz')
out_bval_file = os.path.join(
self.derivatives_directory, 'cmp', self.subject,
self.global_conf.subject_session, 'dwi',
subject + '_dwi.bval')
out_bvec_file = os.path.join(
self.derivatives_directory, 'cmp', self.subject,
self.global_conf.subject_session, 'dwi',
subject + '_dwi.bvec')
if not os.path.isfile(out_dwi_file):
shutil.copy(src=dwi_file, dst=out_dwi_file)
if not os.path.isfile(out_bvec_file):
shutil.copy(src=bvec_file, dst=out_bvec_file)
if not os.path.isfile(out_bval_file):
shutil.copy(src=bval_file, dst=out_bval_file)
valid_inputs = True
input_message = 'Inputs check finished successfully.\nDiffusion and morphological data available.'
else:
input_message = 'Error during inputs check.\nDiffusion bvec or bval files not available.'
else:
if self.global_conf.subject_session == '':
input_message = 'Error during inputs check. No diffusion data available in folder ' + os.path.join(
self.base_directory, self.subject, 'dwi') + '!'
else:
input_message = 'Error during inputs check. No diffusion data available in folder ' + os.path.join(
self.base_directory, self.subject,
self.global_conf.subject_session, 'dwi') + '!'
if gui:
# input_notification = Check_Input_Notification(message=input_message,
# diffusion_imaging_model_options=diffusion_imaging_model,
# diffusion_imaging_model=diffusion_imaging_model)
# input_notification.configure_traits()
print(input_message)
self.global_conf.diffusion_imaging_model = self.diffusion_imaging_model
self.stages[
'Registration'].config.diffusion_imaging_model = self.diffusion_imaging_model
self.stages[
'Diffusion'].config.diffusion_imaging_model = self.diffusion_imaging_model
else:
print(input_message)
self.global_conf.diffusion_imaging_model = self.diffusion_imaging_model
self.stages[
'Registration'].config.diffusion_imaging_model = self.diffusion_imaging_model
self.stages[
'Diffusion'].config.diffusion_imaging_model = self.diffusion_imaging_model
if diffusion_available:
valid_inputs = True
else:
print("Missing required inputs.")
error(
message=
"Missing diffusion inputs. Please see documentation for more details.",
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
# for stage in self.stages.values():
# if stage.enabled:
# print stage.name
# print stage.stage_dir
# self.fill_stages_outputs()
return valid_inputs
class fMRIPipelineUI(fMRIPipeline):
"""Class that extends the :class:`~cmp.pipelines.functional.fMRI.fMRIPipeline` with graphical components.
Attributes
----------
preprocessing : traits.ui.Button
Button to open the window for configuration or quality inspection
of the preprocessing stage depending on the ``view_mode``
registration : traits.ui.Button
Button to open the window for configuration or quality inspection
of the registration stage depending on the ``view_mode``
functionalMRI : traits.ui.Button
Button to open the window for configuration or quality inspection
of the extra preprocessing stage stage depending on the ``view_mode``
connectome : traits.ui.Button
Button to open the window for configuration or quality inspection
of the connectome stage depending on the ``view_mode``
view_mode : ['config_view', 'inspect_outputs_view']
Variable used to control the display of either (1) the configuration
or (2) the quality inspection of stage of the pipeline
pipeline_group : traitsUI panel
Panel defining the layout of the buttons of the stages with corresponding images
traits_view : QtView
QtView that includes the ``pipeline_group`` panel
See also
---------
cmp.pipelines.functional.fMRI.fMRIPipeline
"""
view_mode = Enum('config_view', ['config_view', 'inspect_outputs_view'])
preprocessing = Button('Preprocessing')
functionalMRI = Button('FunctionalMRI')
registration = Button('Registration')
connectome = Button('Connectome')
pipeline_group = VGroup(
HGroup(spring, UItem('preprocessing', style='custom', width=222, height=129, resizable=False,
style_sheet=return_button_style_sheet(ImageResource('preprocessing').absolute_path)), spring,
show_labels=False, label=""),
HGroup(spring, UItem('registration', style='custom', width=222, height=129, resizable=False,
style_sheet=return_button_style_sheet(ImageResource('registration').absolute_path)), spring,
show_labels=False, label=""),
HGroup(spring, UItem('functionalMRI', style='custom', width=222, height=168, resizable=False,
style_sheet=return_button_style_sheet(ImageResource('functionalMRI').absolute_path)), spring,
show_labels=False, label=""),
HGroup(spring, UItem('connectome', style='custom', width=222, height=129, resizable=False,
style_sheet=return_button_style_sheet(ImageResource('connectome').absolute_path)), spring,
show_labels=False, label=""),
spring,
springy=True
)
traits_view = QtView(Include('pipeline_group'))
def __init__(self, project_info):
"""Constructor of the fMRIPipelineUI class.
Parameters
-----------
project_info : cmp.project.CMP_Project_Info
CMP_Project_Info object that stores general information
such as the BIDS root and output directories (see
:class_`cmp.project.CMP_Project_Info` for more details)
See also
---------
cmp.pipelines.functional.fMRIPipeline.__init__
"""
fMRIPipeline.__init__(self, project_info)
self.stages = {'Preprocessing': PreprocessingStageUI(bids_dir=project_info.base_directory,
output_dir=project_info.output_directory),
'Registration': RegistrationStageUI(pipeline_mode="fMRI",
fs_subjects_dir=project_info.freesurfer_subjects_dir,
fs_subject_id=os.path.basename(project_info.freesurfer_subject_id),
bids_dir=project_info.base_directory,
output_dir=self.output_directory),
'FunctionalMRI': FunctionalMRIStageUI(bids_dir=project_info.base_directory,
output_dir=project_info.output_directory),
'Connectome': ConnectomeStageUI(bids_dir=project_info.base_directory,
output_dir=project_info.output_directory)
}
for stage in list(self.stages.keys()):
if project_info.subject_session != '':
self.stages[stage].stage_dir = os.path.join(self.base_directory, "derivatives", 'nipype', self.subject,
project_info.subject_session, self.pipeline_name,
self.stages[stage].name)
else:
self.stages[stage].stage_dir = os.path.join(self.base_directory, "derivatives", 'nipype', self.subject,
self.pipeline_name, self.stages[stage].name)
def _preprocessing_fired(self, info):
"""Method that displays the window for the preprocessing stage.
The window changed accordingly to the value of ``view_mode`` to be
in configuration or quality inspection mode.
Parameters
-----------
info : traits.ui.Button
The preprocessing button object
"""
self.stages['Preprocessing'].configure_traits(view=self.view_mode)
def _functionalMRI_fired(self, info):
"""Method that displays the window for the extra preprocessing stage.
The window changed accordingly to the value of ``view_mode`` to be
in configuration or quality inspection mode.
Parameters
-----------
info : traits.ui.Button
The extra preprocessing button object
"""
self.stages['FunctionalMRI'].configure_traits(view=self.view_mode)
def _registration_fired(self, info):
"""Method that displays the window for the registration stage.
The window changed accordingly to the value of ``view_mode`` to be
in configuration or quality inspection mode.
Parameters
-----------
info : traits.ui.Button
The registration button object
"""
if self.view_mode == 'config_view':
self.stages['Registration'].configure_traits(
view='config_view_fmri')
else:
self.stages['Registration'].configure_traits(view=self.view_mode)
def _connectome_fired(self, info):
"""Method that displays the window for the connectome stage.
The window changed accordingly to the value of ``view_mode`` to be
in configuration or quality inspection mode.
Parameters
-----------
info : traits.ui.Button
The connectome button object
"""
self.stages['Connectome'].configure_traits(view=self.view_mode)
def check_input(self, layout, gui=True):
"""Method that checks if inputs of the fMRI pipeline are available in the datasets.
Parameters
-----------
layout : bids.BIDSLayout
BIDSLayout object used to query
gui : bool
If True, display message in GUI
Returns
-------
valid_inputs : bool
True in all inputs of the fMRI pipeline are available
"""
print('**** Check Inputs ****')
fMRI_available = False
fMRI_json_available = False
t1_available = False
t2_available = False
valid_inputs = False
if self.global_conf.subject_session == '':
subject = self.subject
else:
subject = "_".join(
(self.subject, self.global_conf.subject_session))
fmri_file = os.path.join(
self.subject_directory, 'func', subject + '_task-rest_bold.nii.gz')
json_file = os.path.join(
self.subject_directory, 'func', subject + '_task-rest_bold.json')
t1_file = os.path.join(self.subject_directory,
'anat', subject + '_T1w.nii.gz')
t2_file = os.path.join(self.subject_directory,
'anat', subject + '_T2w.nii.gz')
subjid = self.subject.split("-")[1]
print("Looking for....")
if self.global_conf.subject_session == '':
files = layout.get(subject=subjid, suffix='bold',
extensions='.nii.gz')
if len(files) > 0:
fmri_file = os.path.join(files[0].dirname, files[0].filename)
print(fmri_file)
else:
error(message="BOLD image not found for subject %s." % subjid, title="Error",
buttons=['OK', 'Cancel'], parent=None)
return
files = layout.get(
subject=subjid, suffix='bold', extensions='.json')
if len(files) > 0:
json_file = os.path.join(files[0].dirname, files[0].filename)
print(json_file)
else:
error(message="BOLD json sidecar not found for subject %s." % subjid, title="Warning",
buttons=['OK', 'Cancel'], parent=None)
files = layout.get(subject=subjid, suffix='T1w',
extensions='.nii.gz')
if len(files) > 0:
t1_file = os.path.join(files[0].dirname, files[0].filename)
print(t1_file)
else:
error(message="T1w image not found for subject %s." % subjid, title="Error", buttons=['OK', 'Cancel'],
parent=None)
return
files = layout.get(subject=subjid, suffix='T2w',
extensions='.nii.gz')
if len(files) > 0:
t2_file = os.path.join(files[0].dirname, files[0].filename)
print(t2_file)
else:
error(message="T2w image not found for subject %s." % subjid, title="Warning",
buttons=['OK', 'Cancel'], parent=None)
else:
sessid = self.global_conf.subject_session.split("-")[1]
files = layout.get(subject=subjid, suffix='bold',
extensions='.nii.gz', session=sessid)
if len(files) > 0:
fmri_file = os.path.join(files[0].dirname, files[0].filename)
print(fmri_file)
else:
error(message="BOLD image not found for subject %s, session %s." % (
subjid, self.global_conf.subject_session), title="Error", buttons=['OK', 'Cancel'], parent=None)
return
files = layout.get(subject=subjid, suffix='bold',
extensions='.json', session=sessid)
if len(files) > 0:
json_file = os.path.join(files[0].dirname, files[0].filename)
print(json_file)
else:
error(message="BOLD json sidecar not found for subject %s, session %s." % (
subjid, self.global_conf.subject_session), title="Warning", buttons=['OK', 'Cancel'], parent=None)
files = layout.get(subject=subjid, suffix='T1w',
extensions='.nii.gz', session=sessid)
if len(files) > 0:
t1_file = os.path.join(files[0].dirname, files[0].filename)
print(t1_file)
else:
error(message="T1w image not found for subject %s, session %s." % (
subjid, self.global_conf.subject_session), title="Error", buttons=['OK', 'Cancel'], parent=None)
return
files = layout.get(subject=subjid, suffix='T2w',
extensions='.nii.gz', session=sessid)
if len(files) > 0:
t2_file = os.path.join(files[0].dirname, files[0].filename)
print(t2_file)
else:
error(message="T2w image not found for subject %s, session %s." % (
subjid, self.global_conf.subject_session), title="Warning", buttons=['OK', 'Cancel'], parent=None)
print("fmri_file : %s" % fmri_file)
print("json_file : %s" % json_file)
print("t1_file : %s" % t1_file)
print("t2_file : %s" % t2_file)
if os.path.isfile(t1_file):
# print("%s available" % typ)
t1_available = True
if os.path.isfile(t2_file):
# print("%s available" % typ)
t2_available = True
if os.path.isfile(fmri_file):
# print("%s available" % typ)
fMRI_available = True
if os.path.isfile(json_file):
# print("%s available" % typ)
fMRI_json_available = True
if fMRI_available:
if self.global_conf.subject_session == '':
out_dir = os.path.join(
self.output_directory, 'cmp', self.subject)
else:
out_dir = os.path.join(
self.output_directory, 'cmp', self.subject, self.global_conf.subject_session)
out_fmri_file = os.path.join(
out_dir, 'func', subject + '_task-rest_desc-cmp_bold.nii.gz')
shutil.copy(src=fmri_file, dst=out_fmri_file)
valid_inputs = True
input_message = 'Inputs check finished successfully.\nfMRI data available.'
if t2_available:
out_t2_file = os.path.join(
out_dir, 'anat', subject + '_T2w.nii.gz')
shutil.copy(src=t2_file, dst=out_t2_file)
# swap_and_reorient(src_file=os.path.join(self.base_directory,'NIFTI','T2_orig.nii.gz'),
# ref_file=os.path.join(self.base_directory,'NIFTI','fMRI.nii.gz'),
# out_file=os.path.join(self.base_directory,'NIFTI','T2.nii.gz'))
if fMRI_json_available:
out_json_file = os.path.join(
out_dir, 'func', subject + '_task-rest_desc-cmp_bold.json')
shutil.copy(src=json_file, dst=out_json_file)
else:
input_message = 'Error during inputs check. \nfMRI data not available (fMRI).'
print(input_message)
# if gui:
# # input_notification = Check_Input_Notification(message=input_message, imaging_model='fMRI')
# # input_notification.configure_traits()
# self.global_conf.imaging_model = input_notification.imaging_model
# self.stages['Registration'].config.imaging_model = input_notification.imaging_model
# else:
# self.global_conf.imaging_model = 'fMRI'
# self.stages['Registration'].config.imaging_model = 'fMRI'
self.global_conf.imaging_model = 'fMRI'
self.stages['Registration'].config.imaging_model = 'fMRI'
if t2_available:
self.stages['Registration'].config.registration_mode_trait = [
'FSL (Linear)', 'BBregister (FS)']
else:
self.stages['Registration'].config.registration_mode_trait = [
'FSL (Linear)']
# self.fill_stages_outputs()
return valid_inputs
class MainWindow(HasTraits):
"""Class that defines the Main window of the Connectome Mapper 3 GUI.
Attributes
----------
project_info : cmp.bidsappmanager.project.ProjectInfoUI
Instance of :class:`CMP_Project_InfoUI` that represents the processing project
anat_pipeline : Instance(HasTraits)
Instance of anatomical MRI pipeline UI
dmri_pipeline : Instance(HasTraits)
Instance of diffusion MRI pipeline UI
fmri_pipeline : Instance(HasTraits)
Instance of functional MRI pipeline UI
configurator_ui : `PipelineConfiguratorWindow`
Instance of :class:`PipelineConfiguratorWindow`
bidsapp_ui : `BIDSAppInterfaceWindow`
Instance of :class:`BIDSAppInterfaceWindow`
quality_control_ui : `QualityInspectorWindow`
Instance of :class:`QualityInspectorWindow`
load_dataset : traits.ui.Action
TraitsUI Action to load a BIDS dataset
bidsapp : traits.ui.Button
Button that displays the BIDS App Interface window
configurator : traits.ui.Button
Button thats displays the pipeline Configurator window
quality_control : traits.ui.Button
Button that displays the pipeline Quality Control / Inspector window
manager_group : traits.ui.View
TraitsUI View that describes the content of the main window
traits_view : QtView
TraitsUI QtView that includes ``manager_group`` and parameterize
the window with menu
"""
project_info = Instance(cmp.project.ProjectInfo)
anat_pipeline = Instance(HasTraits)
dmri_pipeline = Instance(HasTraits)
fmri_pipeline = Instance(HasTraits)
configurator_ui = Instance(
cmp.bidsappmanager.gui.config.PipelineConfiguratorWindow)
bidsapp_ui = Instance(
cmp.bidsappmanager.gui.bidsapp.BIDSAppInterfaceWindow)
quality_control_ui = Instance(
cmp.bidsappmanager.gui.qc.QualityInspectorWindow)
load_dataset = Action(name="Load BIDS Dataset...", action="load_dataset")
project_info.style_sheet = style_sheet
configurator = Button("")
bidsapp = Button("")
quality_control = Button("")
view_mode = 1
manager_group = VGroup(
spring,
HGroup(
spring,
HGroup(
Item(
"configurator",
style="custom",
width=200,
height=200,
resizable=False,
label="",
show_label=False,
style_sheet=return_button_style_sheet(
ImageResource(
pkg_resources.resource_filename(
"cmp",
os.path.join("bidsappmanager/images",
"configurator_200x200.png"),
)).absolute_path),
),
show_labels=False,
label="",
),
spring,
HGroup(
Item(
"bidsapp",
style="custom",
width=200,
height=200,
resizable=False,
style_sheet=return_button_style_sheet(
ImageResource(
pkg_resources.resource_filename(
"cmp",
os.path.join("bidsappmanager/images",
"bidsapp_200x200.png"),
)).absolute_path),
),
show_labels=False,
label="",
),
spring,
HGroup(
Item(
"quality_control",
style="custom",
width=200,
height=200,
resizable=False,
style_sheet=return_button_style_sheet(
ImageResource(
pkg_resources.resource_filename(
"cmp",
os.path.join(
"bidsappmanager/images",
"qualitycontrol_200x200.png",
),
)).absolute_path),
),
show_labels=False,
label="",
),
spring,
springy=True,
visible_when="handler.project_loaded==True",
),
spring,
springy=True,
)
traits_view = QtView(
HGroup(Include("manager_group"), ),
title="Connectome Mapper {} - BIDS App Manager".format(__version__),
menubar=MenuBar(
Menu(
ActionGroup(load_dataset, ),
ActionGroup(Action(name="Quit", action="_on_close"), ),
name="File",
), ),
handler=cmp.bidsappmanager.gui.handlers.MainWindowHandler(),
style_sheet=style_sheet,
width=0.5,
height=0.8,
resizable=True, # , scrollable=True , resizable=True
# icon=get_icon("cmp.png")
)
def _bidsapp_fired(self):
""" Callback of the "bidsapp" button. This displays the BIDS App Interface window."""
print_blue("[Open BIDS App Window]")
bids_layout = BIDSLayout(self.project_info.base_directory)
subjects = bids_layout.get_subjects()
anat_config = os.path.join(self.project_info.base_directory, "code/",
"ref_anatomical_config.json")
dmri_config = os.path.join(self.project_info.base_directory, "code/",
"ref_diffusion_config.json")
fmri_config = os.path.join(self.project_info.base_directory, "code/",
"ref_fMRI_config.json")
self.bidsapp_ui = cmp.bidsappmanager.gui.bidsapp.BIDSAppInterfaceWindow(
project_info=self.project_info,
bids_root=self.project_info.base_directory,
subjects=sorted(subjects),
anat_config=anat_config,
dmri_config=dmri_config,
fmri_config=fmri_config,
)
self.bidsapp_ui.configure_traits()
def _configurator_fired(self):
"""Callback of the "configurator" button. This displays the Configurator Window."""
print_blue("[Open Pipeline Configurator Window]")
if self.project_info.t1_available:
if os.path.isfile(self.project_info.anat_config_file):
print(" .. Anatomical config file : %s" %
self.project_info.anat_config_file)
if self.project_info.dmri_available:
if os.path.isfile(self.project_info.dmri_config_file):
print(" .. Diffusion config file : %s" %
self.project_info.dmri_config_file)
if self.project_info.fmri_available:
if os.path.isfile(self.project_info.fmri_config_file):
print(" .. fMRI config file : %s" %
self.project_info.fmri_config_file)
self.configurator_ui = cmp.bidsappmanager.gui.config.PipelineConfiguratorWindow(
project_info=self.project_info,
anat_pipeline=self.anat_pipeline,
dmri_pipeline=self.dmri_pipeline,
fmri_pipeline=self.fmri_pipeline,
anat_inputs_checked=self.project_info.t1_available,
dmri_inputs_checked=self.project_info.dmri_available,
fmri_inputs_checked=self.project_info.fmri_available,
)
self.configurator_ui.configure_traits()
def _quality_control_fired(self):
"""Callback of the "Inspector" button. This displays the Quality Control (Inspector) Window."""
print_blue("[Open Quality Inspector Window]")
if self.project_info.t1_available:
if os.path.isfile(self.project_info.anat_config_file):
print(" .. Anatomical config file : %s" %
self.project_info.anat_config_file)
if self.project_info.dmri_available:
if os.path.isfile(self.project_info.dmri_config_file):
print(" .. Diffusion config file : %s" %
self.project_info.dmri_config_file)
if self.project_info.fmri_available:
if os.path.isfile(self.project_info.fmri_config_file):
print(" .. fMRI config file : %s" %
self.project_info.fmri_config_file)
try:
self.quality_control_ui = cmp.bidsappmanager.gui.qc.QualityInspectorWindow(
project_info=self.project_info,
anat_inputs_checked=self.project_info.t1_available,
dmri_inputs_checked=self.project_info.dmri_available,
fmri_inputs_checked=self.project_info.fmri_available,
)
self.quality_control_ui.configure_traits()
except Exception as e:
print(e)
class fMRIPipelineUI(fMRIPipeline):
view_mode = Enum('config_view', ['config_view', 'inspect_outputs_view'])
preprocessing = Button('Preprocessing')
functionalMRI = Button('FunctionalMRI')
registration = Button('Registration')
connectome = Button('Connectome')
pipeline_group = VGroup(HGroup(spring,
UItem('preprocessing',
style='custom',
width=450,
height=130,
resizable=True,
editor_args={
'image':
ImageResource('preprocessing'),
'label':
""
}),
spring,
show_labels=False,
label=""),
HGroup(spring,
UItem('registration',
style='custom',
width=500,
height=110,
resizable=True,
editor_args={
'image':
ImageResource('registration'),
'label': ""
}),
spring,
show_labels=False,
label=""),
HGroup(spring,
UItem('functionalMRI',
style='custom',
width=450,
height=240,
resizable=True,
editor_args={
'image':
ImageResource('functionalMRI'),
'label':
""
}),
spring,
show_labels=False,
label=""),
HGroup(spring,
UItem('connectome',
style='custom',
width=450,
height=130,
resizable=True,
editor_args={
'image':
ImageResource('connectome'),
'label': ""
}),
spring,
show_labels=False,
label=""),
spring,
springy=True)
traits_view = QtView(Include('pipeline_group'))
def __init__(self, project_info):
fMRIPipeline.__init__(self, project_info)
self.stages = {
'Preprocessing':
PreprocessingStageUI(bids_dir=project_info.base_directory,
output_dir=project_info.output_directory),
'Registration':
RegistrationStageUI(
pipeline_mode="fMRI",
fs_subjects_dir=project_info.freesurfer_subjects_dir,
fs_subject_id=os.path.basename(
project_info.freesurfer_subject_id),
bids_dir=project_info.base_directory,
output_dir=self.output_directory),
'FunctionalMRI':
FunctionalMRIStageUI(bids_dir=project_info.base_directory,
output_dir=project_info.output_directory),
'Connectome':
ConnectomeStageUI(bids_dir=project_info.base_directory,
output_dir=project_info.output_directory)
}
for stage in list(self.stages.keys()):
if project_info.subject_session != '':
self.stages[stage].stage_dir = os.path.join(
self.base_directory, "derivatives", 'nipype', self.subject,
project_info.subject_session, self.pipeline_name,
self.stages[stage].name)
else:
self.stages[stage].stage_dir = os.path.join(
self.base_directory, "derivatives", 'nipype', self.subject,
self.pipeline_name, self.stages[stage].name)
def _preprocessing_fired(self, info):
# print("preproc fired")
self.stages['Preprocessing'].configure_traits(view=self.view_mode)
def _functionalMRI_fired(self, info):
# print("func fired")
self.stages['FunctionalMRI'].configure_traits(view=self.view_mode)
def _registration_fired(self, info):
if self.view_mode == 'config_view':
self.stages['Registration'].configure_traits(
view='config_view_fmri')
else:
self.stages['Registration'].configure_traits(view=self.view_mode)
def _connectome_fired(self, info):
self.stages['Connectome'].configure_traits(view=self.view_mode)
def check_input(self, layout, gui=True):
print('**** Check Inputs ****')
fMRI_available = False
fMRI_json_available = False
t1_available = False
t2_available = False
valid_inputs = False
if self.global_conf.subject_session == '':
subject = self.subject
else:
subject = "_".join(
(self.subject, self.global_conf.subject_session))
fmri_file = os.path.join(self.subject_directory, 'func',
subject + '_task-rest_bold.nii.gz')
json_file = os.path.join(self.subject_directory, 'func',
subject + '_task-rest_bold.json')
t1_file = os.path.join(self.subject_directory, 'anat',
subject + '_T1w.nii.gz')
t2_file = os.path.join(self.subject_directory, 'anat',
subject + '_T2w.nii.gz')
subjid = self.subject.split("-")[1]
print("Looking for....")
if self.global_conf.subject_session == '':
files = layout.get(subject=subjid,
suffix='bold',
extensions='.nii.gz')
if len(files) > 0:
fmri_file = os.path.join(files[0].dirname, files[0].filename)
print(fmri_file)
else:
error(message="BOLD image not found for subject %s." %
(subjid),
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
return
files = layout.get(subject=subjid,
suffix='bold',
extensions='.json')
if len(files) > 0:
json_file = os.path.join(files[0].dirname, files[0].filename)
print(json_file)
else:
error(message="BOLD json sidecar not found for subject %s." %
(subjid),
title="Warning",
buttons=['OK', 'Cancel'],
parent=None)
files = layout.get(subject=subjid,
suffix='T1w',
extensions='.nii.gz')
if len(files) > 0:
t1_file = os.path.join(files[0].dirname, files[0].filename)
print(t1_file)
else:
error(message="T1w image not found for subject %s." % (subjid),
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
return
files = layout.get(subject=subjid,
suffix='T2w',
extensions='.nii.gz')
if len(files) > 0:
t2_file = os.path.join(files[0].dirname, files[0].filename)
print(t2_file)
else:
error(message="T2w image not found for subject %s." % (subjid),
title="Warning",
buttons=['OK', 'Cancel'],
parent=None)
else:
sessid = self.global_conf.subject_session.split("-")[1]
files = layout.get(subject=subjid,
suffix='bold',
extensions='.nii.gz',
session=sessid)
if len(files) > 0:
fmri_file = os.path.join(files[0].dirname, files[0].filename)
print(fmri_file)
else:
error(
message="BOLD image not found for subject %s, session %s."
% (subjid, self.global_conf.subject_session),
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
return
files = layout.get(subject=subjid,
suffix='bold',
extensions='.json',
session=sessid)
if len(files) > 0:
json_file = os.path.join(files[0].dirname, files[0].filename)
print(json_file)
else:
error(
message=
"BOLD json sidecar not found for subject %s, session %s." %
(subjid, self.global_conf.subject_session),
title="Warning",
buttons=['OK', 'Cancel'],
parent=None)
files = layout.get(subject=subjid,
suffix='T1w',
extensions='.nii.gz',
session=sessid)
if len(files) > 0:
t1_file = os.path.join(files[0].dirname, files[0].filename)
print(t1_file)
else:
error(
message="T1w image not found for subject %s, session %s." %
(subjid, self.global_conf.subject_session),
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
return
files = layout.get(subject=subjid,
suffix='T2w',
extensions='.nii.gz',
session=sessid)
if len(files) > 0:
t2_file = os.path.join(files[0].dirname, files[0].filename)
print(t2_file)
else:
error(
message="T2w image not found for subject %s, session %s." %
(subjid, self.global_conf.subject_session),
title="Warning",
buttons=['OK', 'Cancel'],
parent=None)
print("fmri_file : %s" % fmri_file)
print("json_file : %s" % json_file)
print("t1_file : %s" % t1_file)
print("t2_file : %s" % t2_file)
if os.path.isfile(t1_file):
# print("%s available" % typ)
t1_available = True
if os.path.isfile(t2_file):
# print("%s available" % typ)
t2_available = True
if os.path.isfile(fmri_file):
# print("%s available" % typ)
fMRI_available = True
if os.path.isfile(json_file):
# print("%s available" % typ)
fMRI_json_available = True
# print('fMRI :',fMRI_available)
# print('t1 :',t1_available)
# print('t2 :',t2_available)
if fMRI_available:
if self.global_conf.subject_session == '':
out_dir = os.path.join(self.output_directory, 'cmp',
self.subject)
else:
out_dir = os.path.join(self.output_directory, 'cmp',
self.subject,
self.global_conf.subject_session)
out_fmri_file = os.path.join(
out_dir, 'func', subject + '_task-rest_desc-cmp_bold.nii.gz')
shutil.copy(src=fmri_file, dst=out_fmri_file)
valid_inputs = True
input_message = 'Inputs check finished successfully.\nfMRI data available.'
if t2_available:
out_t2_file = os.path.join(out_dir, 'anat',
subject + '_T2w.nii.gz')
shutil.copy(src=t2_file, dst=out_t2_file)
# swap_and_reorient(src_file=os.path.join(self.base_directory,'NIFTI','T2_orig.nii.gz'),
# ref_file=os.path.join(self.base_directory,'NIFTI','fMRI.nii.gz'),
# out_file=os.path.join(self.base_directory,'NIFTI','T2.nii.gz'))
if fMRI_json_available:
out_json_file = os.path.join(
out_dir, 'func', subject + '_task-rest_desc-cmp_bold.json')
shutil.copy(src=json_file, dst=out_json_file)
else:
input_message = 'Error during inputs check. \nfMRI data not available (fMRI).'
print(input_message)
# if gui:
# # input_notification = Check_Input_Notification(message=input_message, imaging_model='fMRI')
# # input_notification.configure_traits()
# self.global_conf.imaging_model = input_notification.imaging_model
# self.stages['Registration'].config.imaging_model = input_notification.imaging_model
# else:
# self.global_conf.imaging_model = 'fMRI'
# self.stages['Registration'].config.imaging_model = 'fMRI'
self.global_conf.imaging_model = 'fMRI'
self.stages['Registration'].config.imaging_model = 'fMRI'
if t2_available:
self.stages['Registration'].config.registration_mode_trait = [
'FSL (Linear)', 'BBregister (FS)'
]
else:
self.stages['Registration'].config.registration_mode_trait = [
'FSL (Linear)'
]
# self.fill_stages_outputs()
return valid_inputs
class DiffusionPipelineUI(DiffusionPipeline):
view_mode = Enum('config_view', ['config_view', 'inspect_outputs_view'])
preprocessing = Button('Preprocessing')
# preprocessing.setIcon(QIcon(QPixmap("preprocessing.png")))
diffusion = Button('Diffusion')
# diffusion.setIcon(QIcon(QPixmap("diffusion.png")))
registration = Button('Registration')
# registration.setIcon(QIcon(QPixmap("registration.png")))
connectome = Button('Connectome')
# connectome.setIcon(QIcon(QPixmap("connectome.png")))
pipeline_group = VGroup(HGroup(spring,
UItem('preprocessing',
style='custom',
width=444,
height=196,
editor_args={
'image':
ImageResource('preprocessing'),
'label':
""
}),
spring,
show_labels=False,
label=""),
HGroup(spring,
UItem('registration',
style='custom',
width=444,
height=196,
editor_args={
'image':
ImageResource('registration'),
'label': ""
}),
spring,
show_labels=False,
label=""),
HGroup(spring,
UItem('diffusion',
style='custom',
width=460,
height=374,
editor_args={
'image':
ImageResource('diffusion'),
'label': ""
}),
spring,
show_labels=False,
label=""),
HGroup(spring,
UItem('connectome',
style='custom',
width=444,
height=184,
editor_args={
'image':
ImageResource('connectome'),
'label': ""
}),
spring,
show_labels=False,
label=""),
springy=True)
traits_view = QtView(Include('pipeline_group'))
def __init__(self, project_info):
DiffusionPipeline.__init__(self, project_info)
self.stages = {
'Preprocessing':
PreprocessingStageUI(bids_dir=project_info.base_directory,
output_dir=project_info.output_directory),
'Registration':
RegistrationStageUI(
pipeline_mode="Diffusion",
fs_subjects_dir=project_info.freesurfer_subjects_dir,
fs_subject_id=os.path.basename(
project_info.freesurfer_subject_id),
bids_dir=project_info.base_directory,
output_dir=self.output_directory),
'Diffusion':
DiffusionStageUI(bids_dir=project_info.base_directory,
output_dir=project_info.output_directory),
'Connectome':
ConnectomeStageUI(bids_dir=project_info.base_directory,
output_dir=project_info.output_directory)
}
for stage in list(self.stages.keys()):
if project_info.subject_session != '':
self.stages[stage].stage_dir = os.path.join(
self.base_directory, "derivatives", 'nipype', self.subject,
project_info.subject_session, self.pipeline_name,
self.stages[stage].name)
else:
self.stages[stage].stage_dir = os.path.join(
self.base_directory, "derivatives", 'nipype', self.subject,
self.pipeline_name, self.stages[stage].name)
def _preprocessing_fired(self, info):
self.stages['Preprocessing'].configure_traits(view=self.view_mode)
def _diffusion_fired(self, info):
self.stages['Diffusion'].configure_traits(view=self.view_mode)
def _registration_fired(self, info):
self.stages['Registration'].configure_traits(view=self.view_mode)
def _connectome_fired(self, info):
# self.stages['MRTrixConnectome'].configure_traits()
self.stages['Connectome'].configure_traits(view=self.view_mode)
def check_input(self, layout, gui=True):
print('**** Check Inputs ****')
diffusion_available = False
bvecs_available = False
bvals_available = False
valid_inputs = False
if self.global_conf.subject_session == '':
subject = self.subject
else:
subject = "_".join(
(self.subject, self.global_conf.subject_session))
dwi_file = os.path.join(self.subject_directory, 'dwi',
subject + '_dwi.nii.gz')
bval_file = os.path.join(self.subject_directory, 'dwi',
subject + '_dwi.bval')
bvec_file = os.path.join(self.subject_directory, 'dwi',
subject + '_dwi.bvec')
subjid = self.subject.split("-")[1]
try:
layout = BIDSLayout(self.base_directory)
print("Valid BIDS dataset with %s subjects" %
len(layout.get_subjects()))
for subj in layout.get_subjects():
self.global_conf.subjects.append('sub-' + str(subj))
# self.global_conf.subjects = ['sub-'+str(subj) for subj in layout.get_subjects()]
self.global_conf.modalities = [
str(mod) for mod in layout.get_modalities()
]
# mods = layout.get_modalities()
types = layout.get_modalities()
# print "Available modalities :"
# for mod in mods:
# print "-%s" % mod
if self.global_conf.subject_session == '':
files = layout.get(subject=subjid,
suffix='dwi',
extensions='.nii.gz')
if len(files) > 0:
dwi_file = os.path.join(files[0].dirname,
files[0].filename)
print(dwi_file)
else:
error(message="Diffusion image not found for subject %s." %
(subjid),
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
return
files = layout.get(subject=subjid,
suffix='dwi',
extensions='.bval')
if len(files) > 0:
bval_file = os.path.join(files[0].dirname,
files[0].filename)
print(bval_file)
else:
error(
message="Diffusion bval image not found for subject %s."
% (subjid),
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
return
files = layout.get(subject=subjid,
suffix='dwi',
extensions='.bvec')
if len(files) > 0:
bvec_file = os.path.join(files[0].dirname,
files[0].filename)
print(bvec_file)
else:
error(
message="Diffusion bvec image not found for subject %s."
% (subjid),
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
return
else:
sessid = self.global_conf.subject_session.split("-")[1]
files = layout.get(subject=subjid,
suffix='dwi',
extensions='.nii.gz',
session=sessid)
if len(files) > 0:
dwi_file = os.path.join(files[0].dirname,
files[0].filename)
print(dwi_file)
else:
error(
message=
"Diffusion image not found for subject %s, session %s."
% (subjid, self.global_conf.subject_session),
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
return
files = layout.get(subject=subjid,
suffix='dwi',
extensions='.bval',
session=sessid)
if len(files) > 0:
bval_file = os.path.join(files[0].dirname,
files[0].filename)
print(bval_file)
else:
error(
message=
"Diffusion bval image not found for subject %s, session %s."
% (subjid, self.global_conf.subject_session),
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
return
files = layout.get(subject=subjid,
suffix='dwi',
extensions='.bvec',
session=sessid)
if len(files) > 0:
bvec_file = os.path.join(files[0].dirname,
files[0].filename)
print(bvec_file)
else:
error(
message=
"Diffusion bvec image not found for subject %s, session %s."
% (subjid, self.global_conf.subject_session),
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
return
print("Looking for....")
print("dwi_file : %s" % dwi_file)
print("bvecs_file : %s" % bvec_file)
print("bvals_file : %s" % bval_file)
if os.path.isfile(dwi_file):
print("DWI available")
diffusion_available = True
except Exception:
error(
message=
"Invalid BIDS dataset. Please see documentation for more details.",
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
return
if os.path.isfile(bval_file):
bvals_available = True
if os.path.isfile(bvec_file):
bvecs_available = True
if diffusion_available:
if bvals_available and bvecs_available:
self.stages[
'Diffusion'].config.diffusion_imaging_model_choices = self.diffusion_imaging_model
# Copy diffusion data to derivatives / cmp / subject / dwi
if self.global_conf.subject_session == '':
out_dwi_file = os.path.join(self.derivatives_directory,
'cmp', self.subject, 'dwi',
subject + '_dwi.nii.gz')
out_bval_file = os.path.join(self.derivatives_directory,
'cmp', self.subject, 'dwi',
subject + '_dwi.bval')
out_bvec_file = os.path.join(self.derivatives_directory,
'cmp', self.subject, 'dwi',
subject + '_dwi.bvec')
else:
out_dwi_file = os.path.join(
self.derivatives_directory, 'cmp', self.subject,
self.global_conf.subject_session, 'dwi',
subject + '_dwi.nii.gz')
out_bval_file = os.path.join(
self.derivatives_directory, 'cmp', self.subject,
self.global_conf.subject_session, 'dwi',
subject + '_dwi.bval')
out_bvec_file = os.path.join(
self.derivatives_directory, 'cmp', self.subject,
self.global_conf.subject_session, 'dwi',
subject + '_dwi.bvec')
if not os.path.isfile(out_dwi_file):
shutil.copy(src=dwi_file, dst=out_dwi_file)
if not os.path.isfile(out_bvec_file):
shutil.copy(src=bvec_file, dst=out_bvec_file)
if not os.path.isfile(out_bval_file):
shutil.copy(src=bval_file, dst=out_bval_file)
valid_inputs = True
input_message = 'Inputs check finished successfully.\nDiffusion and morphological data available.'
else:
input_message = 'Error during inputs check.\nDiffusion bvec or bval files not available.'
else:
if self.global_conf.subject_session == '':
input_message = 'Error during inputs check. No diffusion data available in folder ' + os.path.join(
self.base_directory, self.subject, 'dwi') + '!'
else:
input_message = 'Error during inputs check. No diffusion data available in folder ' + os.path.join(
self.base_directory, self.subject,
self.global_conf.subject_session, 'dwi') + '!'
# diffusion_imaging_model = diffusion_imaging_model[0]
if gui:
# input_notification = Check_Input_Notification(message=input_message, diffusion_imaging_model_options=diffusion_imaging_model,diffusion_imaging_model=diffusion_imaging_model)
# input_notification.configure_traits()
print(input_message)
self.global_conf.diffusion_imaging_model = self.diffusion_imaging_model
# if diffusion_available:
# n_vol = nib.load(dwi_file).shape[3]
# if self.stages['Preprocessing'].config.end_vol == 0 or self.stages['Preprocessing'].config.end_vol == self.stages['Preprocessing'].config.max_vol or self.stages['Preprocessing'].config.end_vol >= n_vol-1:
# self.stages['Preprocessing'].config.end_vol = n_vol-1
# self.stages['Preprocessing'].config.max_vol = n_vol-1
self.stages[
'Registration'].config.diffusion_imaging_model = self.diffusion_imaging_model
self.stages[
'Diffusion'].config.diffusion_imaging_model = self.diffusion_imaging_model
else:
print(input_message)
self.global_conf.diffusion_imaging_model = self.diffusion_imaging_model
# if diffusion_available:
# n_vol = nib.load(dwi_file).shape[3]
# if self.stages['Preprocessing'].config.end_vol == 0 or self.stages['Preprocessing'].config.end_vol == self.stages['Preprocessing'].config.max_vol or self.stages['Preprocessing'].config.end_vol >= n_vol-1:
# self.stages['Preprocessing'].config.end_vol = n_vol-1
# self.stages['Preprocessing'].config.max_vol = n_vol-1
self.stages[
'Registration'].config.diffusion_imaging_model = self.diffusion_imaging_model
self.stages[
'Diffusion'].config.diffusion_imaging_model = self.diffusion_imaging_model
if (diffusion_available):
valid_inputs = True
else:
print("Missing required inputs.")
error(
message=
"Missing diffusion inputs. Please see documentation for more details.",
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
# for stage in self.stages.values():
# if stage.enabled:
# print stage.name
# print stage.stage_dir
# self.fill_stages_outputs()
return valid_inputs
class AnatomicalPipelineUI(AnatomicalPipeline):
segmentation = Button()
# segmentation.setIcon(QIcon(QPixmap("segmentation.png")))
parcellation = Button()
view_mode = Enum('config_view', ['config_view', 'inspect_outputs_view'])
# parcellation.setIcon(QIcon(QPixmap("parcellation.png")))
# custom_run = Button('Custom...')
# run = Button('Run...')
pipeline_group = VGroup(
HGroup(spring,
UItem('segmentation',
style='custom',
width=450,
height=170,
resizable=True,
editor_args={
'image': ImageResource('segmentation'),
'label': ""
}),
spring,
show_labels=False,
label=""),
# Item('parcellation',editor=CustomEditor(image=ImageResource('parcellation'))),show_labels=False),
HGroup(spring,
UItem('parcellation',
style='custom',
width=450,
height=200,
resizable=True,
editor_args={
'image': ImageResource('parcellation'),
'label': ""
}),
spring,
show_labels=False,
label=""),
spring,
springy=True)
traits_view = QtView(Include('pipeline_group'))
def __init__(self, project_info):
AnatomicalPipeline.__init__(self, project_info)
self.stages = {
'Segmentation':
SegmentationStageUI(bids_dir=project_info.base_directory,
output_dir=project_info.output_directory),
'Parcellation':
ParcellationStageUI(pipeline_mode="Diffusion",
bids_dir=project_info.base_directory,
output_dir=project_info.output_directory)
}
for stage in list(self.stages.keys()):
if project_info.subject_session != '':
self.stages[stage].stage_dir = os.path.join(
self.base_directory, "derivatives", 'nipype', self.subject,
project_info.subject_session, self.pipeline_name,
self.stages[stage].name)
else:
self.stages[stage].stage_dir = os.path.join(
self.base_directory, "derivatives", 'nipype', self.subject,
self.pipeline_name, self.stages[stage].name)
def _segmentation_fired(self, info):
self.stages['Segmentation'].configure_traits(view=self.view_mode)
def _parcellation_fired(self, info):
self.stages['Parcellation'].configure_traits(view=self.view_mode)
def check_input(self, layout, gui=True):
print('**** Check Inputs ****')
t1_available = False
valid_inputs = False
types = layout.get_modalities()
if self.global_conf.subject_session == '':
T1_file = os.path.join(self.subject_directory, 'anat',
self.subject + '_T1w.nii.gz')
else:
subjid = self.subject.split("-")[1]
sessid = self.global_conf.subject_session.split("-")[1]
files = layout.get(subject=subjid,
suffix='T1w',
extensions='.nii.gz',
session=sessid)
if len(files) > 0:
T1_file = files[0].filename
print(T1_file)
else:
error(
message="T1w image not found for subject %s, session %s." %
(subjid, self.global_conf.subject_session),
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
return
print("Looking in %s for...." % self.base_directory)
print("T1_file : %s" % T1_file)
for typ in types:
if typ == 'T1w' and os.path.isfile(T1_file):
print("%s available" % typ)
t1_available = True
if t1_available:
# Copy diffusion data to derivatives / cmp / subject / dwi
if self.global_conf.subject_session == '':
out_T1_file = os.path.join(self.derivatives_directory, 'cmp',
self.subject, 'anat',
self.subject + '_T1w.nii.gz')
else:
out_T1_file = os.path.join(
self.derivatives_directory, 'cmp', self.subject,
self.global_conf.subject_session, 'anat', self.subject +
'_' + self.global_conf.subject_session + '_T1w.nii.gz')
if not os.path.isfile(out_T1_file):
shutil.copy(src=T1_file, dst=out_T1_file)
valid_inputs = True
input_message = 'Inputs check finished successfully. \nOnly anatomical data (T1) available.'
else:
input_message = 'Error during inputs check. No anatomical data available in folder ' + os.path.join(
self.base_directory, self.subject) + '/anat/!'
# diffusion_imaging_model = diffusion_imaging_model[0]
if gui:
# input_notification = Check_Input_Notification(message=input_message, diffusion_imaging_model_options=diffusion_imaging_model,diffusion_imaging_model=diffusion_imaging_model)
# input_notification.configure_traits()
print(input_message)
else:
print(input_message)
if (t1_available):
valid_inputs = True
else:
print("Missing required inputs.")
error(
message=
"Missing required inputs. Please see documentation for more details.",
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
for stage in list(self.stages.values()):
if stage.enabled:
print(stage.name)
print(stage.stage_dir)
# self.fill_stages_outputs()
return valid_inputs
def check_output(self):
t1_available = False
brain_available = False
brainmask_available = False
wm_available = False
roivs_available = False
valid_output = False
subject = self.subject
if self.global_conf.subject_session == '':
anat_deriv_subject_directory = os.path.join(
self.base_directory, "derivatives", "cmp", self.subject,
'anat')
else:
if self.global_conf.subject_session not in subject:
anat_deriv_subject_directory = os.path.join(
self.base_directory, "derivatives", "cmp", subject,
self.global_conf.subject_session, 'anat')
subject = "_".join((subject, self.global_conf.subject_session))
else:
anat_deriv_subject_directory = os.path.join(
self.base_directory, "derivatives", "cmp",
subject.split("_")[0], self.global_conf.subject_session,
'anat')
T1_file = os.path.join(anat_deriv_subject_directory,
subject + '_T1w_head.nii.gz')
brain_file = os.path.join(anat_deriv_subject_directory,
subject + '_T1w_brain.nii.gz')
brainmask_file = os.path.join(anat_deriv_subject_directory,
subject + '_T1w_brainmask.nii.gz')
wm_mask_file = os.path.join(anat_deriv_subject_directory,
subject + '_T1w_class-WM.nii.gz')
roiv_files = glob.glob(anat_deriv_subject_directory + "/" + subject +
"_T1w_parc_scale*.nii.gz")
error_message = ''
if os.path.isfile(T1_file):
t1_available = True
else:
error_message = "Missing anatomical output file %s . Please re-run the anatomical pipeline" % T1_file
print(error_message)
error(message=error_message,
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
if os.path.isfile(brain_file):
brain_available = True
else:
error_message = "Missing anatomical output file %s . Please re-run the anatomical pipeline" % brain_file
print(error_message)
error(message=error_message,
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
if os.path.isfile(brainmask_file):
brainmask_available = True
else:
error_message = "Missing anatomical output file %s . Please re-run the anatomical pipeline" % brainmask_file
print(error_message)
error(message=error_message,
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
if os.path.isfile(wm_mask_file):
wm_available = True
else:
error_message = "Missing anatomical output file %s . Please re-run the anatomical pipeline" % wm_mask_file
print(error_message)
error(message=error_message,
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
cnt1 = 0
cnt2 = 0
for roiv_file in roiv_files:
cnt1 = cnt1 + 1
if os.path.isfile(roiv_file):
cnt2 = cnt2 + 1
if cnt1 == cnt2:
roivs_available = True
else:
error_message = "Missing %g/%g anatomical parcellation output files. Please re-run the anatomical pipeline" % (
cnt1 - cnt2, cnt1)
print(error_message)
error(message=error_message,
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
if t1_available is True and brain_available is True and brainmask_available is True and wm_available is True and roivs_available is True:
print("valid deriv/anat output")
valid_output = True
return valid_output, error_message
class AnatomicalPipelineUI(AnatomicalPipeline):
"""Class that extends the :class:`~cmp.pipelines.anatomical.anatomical.AnatomicalPipeline` with graphical components.
Attributes
----------
segmentation : traits.ui.Button
Button to open the window for configuration or quality inspection
of the segmentation stage depending on the ``view_mode``
parcellation : traits.ui.Button
Button to open the window for configuration or quality inspection
of the segmentation stage depending on the ``view_mode``
view_mode : ['config_view', 'inspect_outputs_view']
Variable used to control the display of either (1) the configuration
or (2) the quality inspection of stage of the pipeline
pipeline_group : traitsUI panel
Panel defining the layout of the buttons of the stages with corresponding images
traits_view : QtView
QtView that includes the ``pipeline_group`` panel
See also
---------
cmp.pipelines.anatomical.anatomical.AnatomicalPipeline
"""
segmentation = Button()
parcellation = Button()
view_mode = Enum("config_view", ["config_view", "inspect_outputs_view"])
pipeline_group = VGroup(
HGroup(
spring,
UItem(
"segmentation",
style="custom",
width=222,
height=129,
resizable=False,
style_sheet=return_button_style_sheet(
ImageResource("segmentation").absolute_path
),
),
spring,
show_labels=False,
label="",
),
# Item('parcellation',editor=CustomEditor(image=ImageResource('parcellation'))),show_labels=False),
HGroup(
spring,
UItem(
"parcellation",
style="custom",
width=222,
height=129,
resizable=False,
style_sheet=return_button_style_sheet(
ImageResource("parcellation").absolute_path
),
),
spring,
show_labels=False,
label="",
),
spring,
springy=True,
)
traits_view = QtView(Include("pipeline_group"))
def __init__(self, project_info):
"""Constructor of the AnatomicalPipelineUI class.
Parameters
-----------
project_info : cmp.project.ProjectInfo
CMP_Project_Info object that stores general information
such as the BIDS root and output directories (see
:class_`cmp.project.CMP_Project_Info` for more details)
See also
---------
cmp.pipelines.anatomical.AnatomicalPipeline.__init__
"""
AnatomicalPipeline.__init__(self, project_info)
if len(project_info.subject_sessions) > 0:
subject_id = "_".join((self.subject, self.global_conf.subject_session))
subject_session = self.global_conf.subject_session
else:
subject_id = self.subject
subject_session = ""
self.stages = {
"Segmentation": SegmentationStageUI(
subject=self.subject,
session=subject_session,
bids_dir=project_info.base_directory,
output_dir=project_info.output_directory,
),
"Parcellation": ParcellationStageUI(
pipeline_mode="Diffusion",
subject=self.subject,
session=subject_session,
bids_dir=project_info.base_directory,
output_dir=project_info.output_directory,
),
}
self.stages["Segmentation"].config.freesurfer_subjects_dir = os.path.join(
self.output_directory, __freesurfer_directory__
)
self.stages["Segmentation"].config.freesurfer_subject_id = os.path.join(
self.output_directory, __freesurfer_directory__, subject_id
)
print(
"Freesurfer subjects directory: "
+ self.stages["Segmentation"].config.freesurfer_subjects_dir
)
for stage in list(self.stages.keys()):
if project_info.subject_session != "":
self.stages[stage].stage_dir = os.path.join(
self.base_directory,
"derivatives",
__nipype_directory__,
self.subject,
project_info.subject_session,
self.pipeline_name,
self.stages[stage].name,
)
else:
self.stages[stage].stage_dir = os.path.join(
self.base_directory,
"derivatives",
__nipype_directory__,
self.subject,
self.pipeline_name,
self.stages[stage].name,
)
self.stages["Segmentation"].config.on_trait_change(
self._update_parcellation, "seg_tool"
)
self.stages["Parcellation"].config.on_trait_change(
self._update_segmentation, "parcellation_scheme"
)
def _update_parcellation(self):
"""Update self.stages['Parcellation'].config.parcellation_scheme when ``seg_tool`` is updated."""
if self.stages["Segmentation"].config.seg_tool == "Custom segmentation":
self.stages["Parcellation"].config.parcellation_scheme = "Custom"
self.stages["Parcellation"].config.parcellation_scheme_editor = ["Custom"]
else:
self.stages["Parcellation"].config.parcellation_scheme = "Lausanne2018"
self.stages["Parcellation"].config.parcellation_scheme_editor = [
"NativeFreesurfer", "Lausanne2018", "Custom"
]
def _update_segmentation(self):
"""Update self.stages['Segmentation'].config.seg_tool when ``parcellation_scheme`` is updated."""
if self.stages["Parcellation"].config.parcellation_scheme == "Custom":
self.stages["Segmentation"].config.seg_tool = "Custom segmentation"
else:
self.stages["Segmentation"].config.seg_tool = "Freesurfer"
def _segmentation_fired(self, info):
"""Method that displays the window for the segmentation stage.
The window changed accordingly to the value of ``view_mode`` to be
in configuration or quality inspection mode.
Parameters
-----------
info : traits.ui.Button
The segmentation button object
"""
self.stages["Segmentation"].configure_traits(view=self.view_mode)
def _parcellation_fired(self, info):
"""Method that displays the window for the parcellation stage.
The window changed accordingly to the value of ``view_mode`` to be
in configuration or quality inspection mode.
Parameters
-----------
info : traits.ui.Button
The parcellation button object
"""
self.stages["Parcellation"].configure_traits(view=self.view_mode)
def check_input(self, layout):
"""Method that checks if inputs of the anatomical pipeline are available in the datasets.
Parameters
-----------
layout : bids.BIDSLayout
BIDSLayout object used to query
Returns
-------
valid_inputs : bool
True in all inputs of the anatomical pipeline are available
"""
print("**** Check Inputs ****")
t1_available = False
valid_inputs = False
types = layout.get_modalities()
subjid = self.subject.split("-")[1]
if self.global_conf.subject_session != "":
sessid = self.global_conf.subject_session.split("-")[1]
files = layout.get(
subject=subjid,
session=None if (self.global_conf.subject_session == "") else sessid,
suffix="T1w",
extension="nii.gz",
)
if len(files) > 0:
T1_file = files[0].filename
print(T1_file)
else:
error(
message="T1w image not found for subject %s, session %s."
% (subjid, self.global_conf.subject_session),
title="Error",
buttons=["OK", "Cancel"],
parent=None,
)
return False
for typ in types:
if typ == "T1w" and os.path.isfile(T1_file):
print("T1_file found: %s" % T1_file)
t1_available = True
if t1_available:
# Copy diffusion data to derivatives / cmp / subject / dwi
if self.global_conf.subject_session == "":
out_T1_file = os.path.join(
self.derivatives_directory, __cmp_directory__,
self.subject, "anat",
self.subject + "_T1w.nii.gz",
)
else:
out_T1_file = os.path.join(
self.derivatives_directory, __cmp_directory__,
self.subject, self.global_conf.subject_session, "anat",
f'{self.subject}_{self.global_conf.subject_session}_T1w.nii.gz',
)
if not os.path.isfile(out_T1_file):
shutil.copy(src=T1_file, dst=out_T1_file)
msg = "Inputs check finished successfully. \nAnatomical data (T1w) available."
print(f'\tINFO: {msg}')
valid_inputs = True
else:
msg = (
" * No anatomical data (T1w) available in folder "
+ os.path.join(self.base_directory, self.subject, 'anat')
+ "!\n"
)
print(f'\tERROR: Missing required inputs: {msg}')
error(
message=f"Missing required inputs:\n{msg} Please see documentation for more details.",
title="Error",
buttons=["OK", "Cancel"],
parent=None,
)
if self.stages["Parcellation"].config.parcellation_scheme == "Custom":
msg = ""
custom_parc_nii_available = True
custom_parc_tsv_available = True
custom_brainmask_available = True
custom_gm_mask_available = True
custom_wm_mask_available = True
custom_csf_mask_available = True
custom_aparcaseg_available = True
# Add custom BIDS derivatives directories to the BIDSLayout
custom_derivatives_dirnames = [
self.stages["Parcellation"].config.custom_parcellation.get_toolbox_derivatives_dir(),
self.stages["Segmentation"].config.custom_brainmask.get_toolbox_derivatives_dir(),
self.stages["Segmentation"].config.custom_gm_mask.get_toolbox_derivatives_dir(),
self.stages["Segmentation"].config.custom_wm_mask.get_toolbox_derivatives_dir(),
self.stages["Segmentation"].config.custom_csf_mask.get_toolbox_derivatives_dir(),
self.stages["Segmentation"].config.custom_aparcaseg.get_toolbox_derivatives_dir()
]
# Keep only unique custom derivatives to make the BIDSLayout happy
custom_derivatives_dirnames = list(set(custom_derivatives_dirnames))
for custom_derivatives_dirname in custom_derivatives_dirnames:
if custom_derivatives_dirname not in layout.derivatives:
print(f" * Add custom_derivatives_dirname: {custom_derivatives_dirname}")
layout.add_derivatives(os.path.join(self.base_directory, 'derivatives', custom_derivatives_dirname))
files = layout.get(
subject=subjid,
session=(None
if self.global_conf.subject_session == ""
else self.global_conf.subject_session.split("-")[1]),
suffix=self.stages["Parcellation"].config.custom_parcellation.suffix,
atlas=self.stages["Parcellation"].config.custom_parcellation.atlas,
resolution=self.stages["Parcellation"].config.custom_parcellation.resolution,
extension="nii.gz",
)
if len(files) > 0:
custom_parc_file = os.path.join(files[0].dirname, files[0].filename)
else:
custom_parc_file = "NotFound"
custom_parc_nii_available = False
print("... custom_parc_file : %s" % custom_parc_file)
files = layout.get(
subject=subjid,
session=(None
if self.global_conf.subject_session == ""
else self.global_conf.subject_session.split("-")[1]),
suffix=self.stages["Parcellation"].config.custom_parcellation.suffix,
extension="tsv",
atlas=self.stages["Parcellation"].config.custom_parcellation.atlas,
resolution=self.stages["Parcellation"].config.custom_parcellation.resolution,
)
if len(files) > 0:
custom_parc_tsv_file = os.path.join(files[0].dirname, files[0].filename)
else:
custom_parc_tsv_file = "NotFound"
msg += f' * Custom parcellation ({self.stages["Parcellation"].config.custom_parcellation}) not found\n'
custom_parc_tsv_available = False
print("... custom_parc_tsv_file : %s" % custom_parc_tsv_file)
if not custom_parc_nii_available and not custom_parc_tsv_available:
valid_inputs = False
files = layout.get(
subject=subjid,
session=(None
if self.global_conf.subject_session == ""
else self.global_conf.subject_session.split("-")[1]),
suffix=self.stages["Segmentation"].config.custom_brainmask.suffix,
extension="nii.gz",
desc=self.stages["Segmentation"].config.custom_brainmask.desc,
)
if len(files) > 0:
custom_brainmask_file = os.path.join(files[0].dirname, files[0].filename)
else:
custom_brainmask_file = "NotFound"
msg += f' * Custom brain mask ({self.stages["Segmentation"].config.custom_brainmask}) not found\n'
custom_brainmask_available = False
print("... custom_brainmask_file : %s" % custom_brainmask_file)
if not custom_brainmask_available:
valid_inputs = False
files = layout.get(
subject=subjid,
session=(None
if self.global_conf.subject_session == ""
else self.global_conf.subject_session.split("-")[1]),
suffix=self.stages["Segmentation"].config.custom_gm_mask.suffix,
extension="nii.gz",
label=self.stages["Segmentation"].config.custom_gm_mask.label,
)
if len(files) > 0:
custom_gm_mask_file = os.path.join(files[0].dirname, files[0].filename)
else:
custom_gm_mask_file = "NotFound"
msg += f' * Custom gray matter mask ({self.stages["Segmentation"].config.custom_gm_mask}) not found\n'
custom_gm_mask_available = False
print("... custom_gm_mask_file : %s" % custom_gm_mask_file)
if not custom_gm_mask_available:
valid_inputs = False
files = layout.get(
subject=subjid,
session=(None
if self.global_conf.subject_session == ""
else self.global_conf.subject_session.split("-")[1]),
suffix=self.stages["Segmentation"].config.custom_wm_mask.suffix,
extension="nii.gz",
label=self.stages["Segmentation"].config.custom_wm_mask.label,
)
if len(files) > 0:
custom_wm_mask_file = os.path.join(files[0].dirname, files[0].filename)
else:
custom_wm_mask_file = "NotFound"
msg += f' * Custom white matter mask ({self.stages["Segmentation"].config.custom_wm_mask}) not found\n'
custom_wm_mask_available = False
print("... custom_wm_mask_file : %s" % custom_wm_mask_file)
if not custom_wm_mask_available:
valid_inputs = False
files = layout.get(
subject=subjid,
session=(None
if self.global_conf.subject_session == ""
else self.global_conf.subject_session.split("-")[1]),
suffix=self.stages["Segmentation"].config.custom_csf_mask.suffix,
extension="nii.gz",
label=self.stages["Segmentation"].config.custom_csf_mask.label,
)
if len(files) > 0:
custom_csf_mask_file = os.path.join(files[0].dirname, files[0].filename)
else:
custom_csf_mask_file = "NotFound"
msg += f' * Custom CSF mask ({self.stages["Segmentation"].config.custom_csf_mask}) not found\n'
custom_csf_mask_available = False
print("... custom_csf_mask_file : %s" % custom_csf_mask_file)
if not custom_csf_mask_available:
valid_inputs = False
files = layout.get(
subject=subjid,
session=(None
if self.global_conf.subject_session == ""
else self.global_conf.subject_session.split("-")[1]),
suffix=self.stages["Segmentation"].config.custom_aparcaseg.suffix,
extension="nii.gz",
desc=self.stages["Segmentation"].config.custom_aparcaseg.desc,
)
if len(files) > 0:
custom_aparcaseg_file = os.path.join(files[0].dirname, files[0].filename)
else:
custom_aparcaseg_file = "NotFound"
msg += f' * Custom Freesurfer\'s aparc+aseg ({self.stages["Segmentation"].config.custom_gm_mask}) not found\n'
custom_aparcaseg_available = False
print("... custom_aparcaseg_file : %s" % custom_aparcaseg_file)
if not custom_aparcaseg_available:
valid_inputs = False
if not valid_inputs:
error(
message=f"Missing required custom inputs:\n{msg} Please see documentation for more details.",
title="Error",
buttons=["OK", "Cancel"],
parent=None,
)
return valid_inputs
def check_output(self):
"""Method that checks if outputs of the anatomical pipeline are available.
Returns
--------
valid_output : bool
True is all outputs are found
error_message : string
Message in case there is an error
"""
t1_available = False
brain_available = False
brainmask_available = False
wm_available = False
roivs_available = False
valid_output = False
subject = self.subject
if self.global_conf.subject_session == "":
anat_deriv_subject_directory = os.path.join(
self.base_directory, "derivatives", __cmp_directory__, self.subject, "anat"
)
else:
if self.global_conf.subject_session not in subject:
anat_deriv_subject_directory = os.path.join(
self.base_directory, "derivatives", __cmp_directory__,
subject, self.global_conf.subject_session, "anat",
)
subject = "_".join((subject, self.global_conf.subject_session))
else:
anat_deriv_subject_directory = os.path.join(
self.base_directory, "derivatives", __cmp_directory__,
subject.split("_")[0], self.global_conf.subject_session, "anat",
)
T1_file = os.path.join(
anat_deriv_subject_directory, subject + "_T1w_head.nii.gz"
)
brain_file = os.path.join(
anat_deriv_subject_directory, subject + "_T1w_brain.nii.gz"
)
brainmask_file = os.path.join(
anat_deriv_subject_directory, subject + "_T1w_brainmask.nii.gz"
)
wm_mask_file = os.path.join(
anat_deriv_subject_directory, subject + "_T1w_class-WM.nii.gz"
)
roiv_files = glob.glob(
anat_deriv_subject_directory + "/" + subject + "_T1w_parc_scale*.nii.gz"
)
error_message = ""
if os.path.isfile(T1_file):
t1_available = True
else:
error_message = (
"Missing anatomical output file %s . Please re-run the anatomical pipeline"
% T1_file
)
print(error_message)
error(
message=error_message,
title="Error",
buttons=["OK", "Cancel"],
parent=None,
)
if os.path.isfile(brain_file):
brain_available = True
else:
error_message = (
"Missing anatomical output file %s . Please re-run the anatomical pipeline"
% brain_file
)
print(error_message)
error(
message=error_message,
title="Error",
buttons=["OK", "Cancel"],
parent=None,
)
if os.path.isfile(brainmask_file):
brainmask_available = True
else:
error_message = (
"Missing anatomical output file %s . Please re-run the anatomical pipeline"
% brainmask_file
)
print(error_message)
error(
message=error_message,
title="Error",
buttons=["OK", "Cancel"],
parent=None,
)
if os.path.isfile(wm_mask_file):
wm_available = True
else:
error_message = (
"Missing anatomical output file %s . Please re-run the anatomical pipeline"
% wm_mask_file
)
print(error_message)
error(
message=error_message,
title="Error",
buttons=["OK", "Cancel"],
parent=None,
)
cnt1 = 0
cnt2 = 0
for roiv_file in roiv_files:
cnt1 = cnt1 + 1
if os.path.isfile(roiv_file):
cnt2 = cnt2 + 1
if cnt1 == cnt2:
roivs_available = True
else:
error_message = (
"Missing %g/%g anatomical parcellation output files. Please re-run the anatomical pipeline"
% (cnt1 - cnt2, cnt1)
)
print(error_message)
error(
message=error_message,
title="Error",
buttons=["OK", "Cancel"],
parent=None,
)
if (
t1_available is True
and brain_available is True
and brainmask_available is True
and wm_available is True
and roivs_available is True
):
print("valid deriv/anat output")
valid_output = True
return valid_output, error_message
class AnatomicalPipelineUI(AnatomicalPipeline):
"""Class that extends the :class:`~cmp.pipelines.anatomical.anatomical.AnatomicalPipeline` with graphical components.
Attributes
----------
segmentation : traits.ui.Button
Button to open the window for configuration or quality inspection
of the segmentation stage depending on the ``view_mode``
parcellation : traits.ui.Button
Button to open the window for configuration or quality inspection
of the segmentation stage depending on the ``view_mode``
view_mode : ['config_view', 'inspect_outputs_view']
Variable used to control the display of either (1) the configuration
or (2) the quality inspection of stage of the pipeline
pipeline_group : traitsUI panel
Panel defining the layout of the buttons of the stages with corresponding images
traits_view : QtView
QtView that includes the ``pipeline_group`` panel
See also
---------
cmp.pipelines.anatomical.anatomical.AnatomicalPipeline
"""
segmentation = Button()
parcellation = Button()
view_mode = Enum('config_view', ['config_view', 'inspect_outputs_view'])
pipeline_group = VGroup(
HGroup(spring,
UItem('segmentation',
style='custom',
width=222,
height=129,
resizable=False,
style_sheet=return_button_style_sheet(
ImageResource('segmentation').absolute_path)),
spring,
show_labels=False,
label=""),
# Item('parcellation',editor=CustomEditor(image=ImageResource('parcellation'))),show_labels=False),
HGroup(spring,
UItem('parcellation',
style='custom',
width=222,
height=129,
resizable=False,
style_sheet=return_button_style_sheet(
ImageResource('parcellation').absolute_path)),
spring,
show_labels=False,
label=""),
spring,
springy=True)
traits_view = QtView(Include('pipeline_group'))
def __init__(self, project_info):
"""Constructor of the AnatomicalPipelineUI class.
Parameters
-----------
project_info : cmp.project.CMP_Project_Info
CMP_Project_Info object that stores general information
such as the BIDS root and output directories (see
:class_`cmp.project.CMP_Project_Info` for more details)
See also
---------
cmp.pipelines.anatomical.AnatomicalPipeline.__init__
"""
AnatomicalPipeline.__init__(self, project_info)
self.stages = {
'Segmentation':
SegmentationStageUI(bids_dir=project_info.base_directory,
output_dir=project_info.output_directory),
'Parcellation':
ParcellationStageUI(pipeline_mode="Diffusion",
bids_dir=project_info.base_directory,
output_dir=project_info.output_directory)
}
if len(project_info.subject_sessions) > 0:
subject_id = "_".join(
(self.subject, self.global_conf.subject_session))
else:
subject_id = self.subject
self.stages[
'Segmentation'].config.freesurfer_subjects_dir = os.path.join(
self.output_directory, 'freesurfer')
self.stages[
'Segmentation'].config.freesurfer_subject_id = os.path.join(
self.output_directory, 'freesurfer', subject_id)
print('Freesurfer subjects directory: ' +
self.stages['Segmentation'].config.freesurfer_subjects_dir)
for stage in list(self.stages.keys()):
if project_info.subject_session != '':
self.stages[stage].stage_dir = os.path.join(
self.base_directory, "derivatives", 'nipype', self.subject,
project_info.subject_session, self.pipeline_name,
self.stages[stage].name)
else:
self.stages[stage].stage_dir = os.path.join(
self.base_directory, "derivatives", 'nipype', self.subject,
self.pipeline_name, self.stages[stage].name)
def _segmentation_fired(self, info):
"""Method that displays the window for the segmentation stage.
The window changed accordingly to the value of ``view_mode`` to be
in configuration or quality inspection mode.
Parameters
-----------
info : traits.ui.Button
The segmentation button object
"""
self.stages['Segmentation'].configure_traits(view=self.view_mode)
def _parcellation_fired(self, info):
"""Method that displays the window for the parcellation stage.
The window changed accordingly to the value of ``view_mode`` to be
in configuration or quality inspection mode.
Parameters
-----------
info : traits.ui.Button
The parcellation button object
"""
self.stages['Parcellation'].configure_traits(view=self.view_mode)
def check_input(self, layout, gui=True):
"""Method that checks if inputs of the anatomical pipeline are available in the datasets.
Parameters
-----------
layout : bids.BIDSLayout
BIDSLayout object used to query
gui : Boolean
If `True` display messages and errors in graphical window
Returns
-------
valid_inputs : bool
True in all inputs of the anatomical pipeline are available
"""
print('**** Check Inputs ****')
t1_available = False
valid_inputs = False
types = layout.get_modalities()
if self.global_conf.subject_session == '':
T1_file = os.path.join(self.subject_directory, 'anat',
self.subject + '_T1w.nii.gz')
else:
subjid = self.subject.split("-")[1]
sessid = self.global_conf.subject_session.split("-")[1]
files = layout.get(subject=subjid,
suffix='T1w',
extensions='.nii.gz',
session=sessid)
if len(files) > 0:
T1_file = files[0].filename
print(T1_file)
else:
error(
message="T1w image not found for subject %s, session %s." %
(subjid, self.global_conf.subject_session),
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
return
print("Looking in %s for...." % self.base_directory)
print("T1_file : %s" % T1_file)
for typ in types:
if typ == 'T1w' and os.path.isfile(T1_file):
print("%s available" % typ)
t1_available = True
if t1_available:
# Copy diffusion data to derivatives / cmp / subject / dwi
if self.global_conf.subject_session == '':
out_T1_file = os.path.join(self.derivatives_directory, 'cmp',
self.subject, 'anat',
self.subject + '_T1w.nii.gz')
else:
out_T1_file = os.path.join(
self.derivatives_directory, 'cmp', self.subject,
self.global_conf.subject_session, 'anat', self.subject +
'_' + self.global_conf.subject_session + '_T1w.nii.gz')
if not os.path.isfile(out_T1_file):
shutil.copy(src=T1_file, dst=out_T1_file)
valid_inputs = True
input_message = 'Inputs check finished successfully. \nOnly anatomical data (T1) available.'
else:
input_message = 'Error during inputs check. No anatomical data available in folder ' + os.path.join(
self.base_directory, self.subject) + '/anat/!'
# diffusion_imaging_model = diffusion_imaging_model[0]
if gui:
# input_notification = Check_Input_Notification(message=input_message,
# diffusion_imaging_model_options=diffusion_imaging_model,
# diffusion_imaging_model=diffusion_imaging_model)
# input_notification.configure_traits()
print(input_message)
else:
print(input_message)
if t1_available:
valid_inputs = True
else:
print("Missing required inputs.")
error(
message=
"Missing required inputs. Please see documentation for more details.",
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
for stage in list(self.stages.values()):
if stage.enabled:
print(stage.name)
print(stage.stage_dir)
# self.fill_stages_outputs()
return valid_inputs
def check_output(self):
"""Method that checks if outputs of the anatomical pipeline are available.
Returns
--------
valid_output : bool
True is all outputs are found
error_message : string
Message in case there is an error
"""
t1_available = False
brain_available = False
brainmask_available = False
wm_available = False
roivs_available = False
valid_output = False
subject = self.subject
if self.global_conf.subject_session == '':
anat_deriv_subject_directory = os.path.join(
self.base_directory, "derivatives", "cmp", self.subject,
'anat')
else:
if self.global_conf.subject_session not in subject:
anat_deriv_subject_directory = os.path.join(
self.base_directory, "derivatives", "cmp", subject,
self.global_conf.subject_session, 'anat')
subject = "_".join((subject, self.global_conf.subject_session))
else:
anat_deriv_subject_directory = os.path.join(
self.base_directory, "derivatives", "cmp",
subject.split("_")[0], self.global_conf.subject_session,
'anat')
T1_file = os.path.join(anat_deriv_subject_directory,
subject + '_T1w_head.nii.gz')
brain_file = os.path.join(anat_deriv_subject_directory,
subject + '_T1w_brain.nii.gz')
brainmask_file = os.path.join(anat_deriv_subject_directory,
subject + '_T1w_brainmask.nii.gz')
wm_mask_file = os.path.join(anat_deriv_subject_directory,
subject + '_T1w_class-WM.nii.gz')
roiv_files = glob.glob(anat_deriv_subject_directory + "/" + subject +
"_T1w_parc_scale*.nii.gz")
error_message = ''
if os.path.isfile(T1_file):
t1_available = True
else:
error_message = "Missing anatomical output file %s . Please re-run the anatomical pipeline" % T1_file
print(error_message)
error(message=error_message,
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
if os.path.isfile(brain_file):
brain_available = True
else:
error_message = "Missing anatomical output file %s . Please re-run the anatomical pipeline" % brain_file
print(error_message)
error(message=error_message,
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
if os.path.isfile(brainmask_file):
brainmask_available = True
else:
error_message = "Missing anatomical output file %s . Please re-run the anatomical pipeline" % brainmask_file
print(error_message)
error(message=error_message,
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
if os.path.isfile(wm_mask_file):
wm_available = True
else:
error_message = "Missing anatomical output file %s . Please re-run the anatomical pipeline" % wm_mask_file
print(error_message)
error(message=error_message,
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
cnt1 = 0
cnt2 = 0
for roiv_file in roiv_files:
cnt1 = cnt1 + 1
if os.path.isfile(roiv_file):
cnt2 = cnt2 + 1
if cnt1 == cnt2:
roivs_available = True
else:
error_message = "Missing %g/%g anatomical parcellation output files. Please re-run the anatomical pipeline" % (
cnt1 - cnt2, cnt1)
print(error_message)
error(message=error_message,
title="Error",
buttons=['OK', 'Cancel'],
parent=None)
if t1_available is True and brain_available is True and brainmask_available is True and wm_available is True and roivs_available is True:
print("valid deriv/anat output")
valid_output = True
return valid_output, error_message