def traits_view(self):
contour_grp = HGroup(Item('color_map_name',
label='Color Map',
editor=EnumEditor(values=sorted(color_map_name_dict.keys()))),
Item('levels'),
Item('marker_size'),
visible_when='plot_kind=="Contour"')
monitor_grp = Item('monitor', editor=EnumEditor(name='monitors'))
v = View(
VGroup(HGroup(UItem('calculate_button'),
UItem('data_source', editor=EnumEditor(values=['database', 'file'])),
monitor_grp),
HGroup(Item('save_mean_j', label='Save Mean J'),
Item('auto_clear_cache', label='Auto Clear Cache')),
Item('mean_j_error_type', label='Mean J Error'),
HGroup(Item('use_weighted_fit'),
Item('use_monte_carlo'),
Item('monte_carlo_ntrials',
enabled_when='object.use_monte_carlo')),
Item('predicted_j_error_type', label='Predicted J Error',
enabled_when='not (object.use_weighted_fit or object.use_monte_carlo)'),
HGroup(Item('group_positions'),
Item('object.monitor.sample',
style='readonly', label='Sample')),
Item('show_labels',
label='Display Labels',
tooltip='Display hole labels on plot'),
HGroup(UItem('plot_kind'),
Item('model_kind', label='Fit Model',
editor=EnumEditor(values=['Bowl', 'Plane']))),
# UItem('plot_kind', editor=EnumEditor(values=['Contour', 'Hole vs J']))),
contour_grp))
return v
def _get_columns(self):
cols = [
ObjectColumn(name='name', editable=False),
CheckboxColumn(name='show'),
CheckboxColumn(name='use', label='Save'),
ObjectColumn(name='fit',
editor=EnumEditor(name='fit_types'),
width=150),
ObjectColumn(name='error_type',
editor=EnumEditor(name='error_types'),
width=50)
]
return cols
def traits_view(self):
contour_grp = VGroup(Item('color_map_name',
label='Color Map',
editor=EnumEditor(values=sorted(color_map_name_dict.keys()))),
Item('levels'),
visible_when='plot_kind=="Contour"')
monitor_grp=Item('monitor', editor=EnumEditor(name='monitors'))
v = View(
VGroup(HGroup(UItem('calculate_button'),
UItem('data_source', editor=EnumEditor(values=['database', 'file'])),
monitor_grp),
HGroup(Item('group_positions'), Item('object.monitor.sample', style='readonly',label='Sample')),
HGroup(UItem('plot_kind'),
Item('model_kind', label='Fit Model',
editor=EnumEditor(values=['Bowl', 'Plane']))),
# UItem('plot_kind', editor=EnumEditor(values=['Contour', 'Hole vs J']))),
contour_grp))
return v
def _get_auto_group(self):
return VGroup(
HGroup(
icon_button_editor(
'plot_button',
'refresh',
tooltip='Replot the isotope evolutions. '
'This may take awhile if many analyses are selected'),
icon_button_editor('save_event',
'database_save',
tooltip='Save fits to database'),
Item(
'auto_update',
label='Auto Plot',
tooltip=
'Should the plot refresh after each change ie. "fit" or "show". '
'It is not advisable to use this option with many analyses'
)),
HGroup(
UItem('global_fit', editor=EnumEditor(name='fit_types')),
UItem('global_error_type',
editor=EnumEditor(name='error_types'))))
def traits_view(self):
v = View(VGroup(
VGroup(
HGroup(
UItem('branch', editor=EnumEditor(name='all_branches')),
icon_button_editor(
'build_button',
'bricks',
tooltip=
'Build selected branch and set as current application'
),
icon_button_editor('checkout_branch_button',
'foo',
tooltip='Checkout selected branch'),
show_border=True,
label='Current Branch')),
VGroup(UItem('edit_branch', editor=EnumEditor(name='branches')),
UItem('delete_button', enabled_when='delete_enabled'),
show_border=True)),
title='Manage Branch View',
buttons=['OK', 'Cancel'])
return v
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")
def __init__(self, parent, my_crystal):
self._init_ctrls(parent)
#Make all the sizers
self.boxSizerAll = wx.BoxSizer(orient=wx.VERTICAL)
self.boxSizerIsaw = wx.BoxSizer(orient=wx.VERTICAL)
self.boxSizerManual = wx.BoxSizer(orient=wx.VERTICAL)
self.boxSizerButtons = wx.BoxSizer(orient=wx.HORIZONTAL)
#Setup the parameter editor traits ui panel
self.original_crystal = my_crystal
self.crystal = copy.copy(my_crystal)
self.handler = CrystalEditorTraitsHandler(self)
#Make the TRAITS view
#At the top is a general view
self.view_top = View(
Group(
Item("name", label="Crystal Name"),
Item("description",
label="Description:",
editor=TextEditor(multi_line=True)),
Item("lattice_lengths_arr",
label="Lattice sizes (Angstroms)",
format_str="%.3f",
style='readonly'),
Item("lattice_angles_deg_arr",
label="Lattice angles (degrees)",
format_str="%.3f",
style='readonly'),
Item("point_group_name",
label="Point Group:",
editor=EnumEditor(name="point_group_name_list")),
Item("reflection_condition_name",
label="Reflection Condition:",
editor=EnumEditor(name="reflection_condition_name_list")),
Item("ub_matrix",
label="Sample's UB Matrix",
style='readonly',
format_str="%9.5f"),
Item("ub_matrix_is_from",
label="UB matrix obtained from",
style='readonly'),
label=""), )
#Make the control and add it
self.control_top = self.crystal.edit_traits(
parent=self,
view=self.view_top,
kind='subpanel',
handler=self.handler).control
self.boxSizerAll.AddWindow(self.control_top,
0,
border=0,
flag=wx.EXPAND)
# Now add the notebook, make it expand
self.boxSizerAll.AddWindow(self.notebook,
1,
border=4,
flag=wx.EXPAND | wx.LEFT | wx.RIGHT
| wx.TOP)
#Now a view to manually create the parameters
angle_label = Group(
Label(
label=
"""If all the sample mounting angles are zero, the sample's crystal
lattice coordinate system is aligned with the instrument coordinates.
The 'a' vector is parallel to x; 'b' is in the XY plane towards +y;
'c' goes towards +z.
""",
emphasized=False,
show_label=True), )
fmt = "%.3f"
self.view_manual = View(
Group(Item("lattice_lengths_arr",
label="Lattice dimensions\n(a,b,c - in Angstroms)",
format_str=fmt),
Item("lattice_angles_deg_arr",
label="Lattice angles\n(alpha,beta,gamma - in degrees)",
format_str=fmt),
Item("valid_parameters_yesno",
label="Lattice is valid?",
style='readonly'),
label="Lattice parameters"),
Spring(label=" ", emphasized=False, show_label=False),
Group(
angle_label,
Item("sample_mount_phi",
label=
"Sample mounting angle phi\n (1st rotation, around Y)",
format_str=fmt),
Item("sample_mount_chi",
label=
"Sample mounting angle chi\n (2nd rotation, around Z)",
format_str=fmt),
Item("sample_mount_omega",
label=
"Sample mounting angle omega\n (3rd rotation, around Y)",
format_str=fmt),
label="Sample mounting"),
resizable=True)
#Make it into a control, put it in the notebook
self.control_manual = self.crystal.edit_traits(
parent=self.panelManual,
view=self.view_manual,
kind='subpanel',
handler=self.handler).control
self.notebook.AddPage(self.panelManual, "Manually Enter Lattice")
self.boxSizerManual.AddWindow(self.control_manual,
0,
border=0,
flag=wx.EXPAND)
self.boxSizerManual.AddSpacer(wx.Size(8, 8))
self.boxSizerManual.AddWindow(self.buttonGenerateUB,
0,
border=0,
flag=wx.CENTER)
self.panelManual.SetSizer(self.boxSizerManual)
self.ub_orientation = SampleOrientationWhenUBMatrixWasSaved()
self.control_load_angles = self.ub_orientation.edit_traits(
parent=self.panelIsaw, kind='subpanel').control
self._init_sizers()
def get_view(self):
return View(Item('stopping_criterion',
editor=EnumEditor(name="criterion_list")),
Item('criterion_value'),
buttons=[OKButton, CancelButton])
def traits_view(self):
add_button = icon_button_editor(
'add_button',
'add',
# enabled_when='ok_add',
tooltip='Add run')
save_button = icon_button_editor('save_button',
'disk',
tooltip='Save queue to file')
edit_button = icon_button_editor('edit_mode_button',
'table_edit',
enabled_when='edit_enabled',
tooltip='Toggle edit mode')
clear_button = icon_button_editor(
'clear_button',
'table_row_delete',
tooltip='Clear all runs added using "frequency"')
email_grp = BorderVGroup(HGroup(
queue_factory_item('use_email',
label='Use Email',
tooltip='Send email notifications'),
queue_factory_item('use_group_email',
tooltip='Email a group of users',
label='Email Group'),
icon_button_editor(queue_factory_name('edit_emails'),
'cog',
tooltip='Edit user group')),
queue_factory_uitem('email', springy=True),
label='Email')
user_grp = BorderHGroup(
UItem(queue_factory_name('username'),
editor=ComboboxEditor(name=queue_factory_name('usernames'))),
icon_button_editor(queue_factory_name('edit_user'),
'database_edit'),
label='User')
load_select = BorderHGroup(
queue_factory_uitem('load_name', width=150),
queue_factory_item(
'tray', editor=EnumEditor(name=queue_factory_name('trays'))),
icon_button_editor(
queue_factory_name('select_existing_load_name_button'),
'database_go',
tooltip='Get Load from Database'),
label='Load')
generate_queue = BorderHGroup(
icon_button_editor(
'generate_queue_button',
'brick-go',
tooltip='Generate a experiment queue from the selected load',
enabled_when='load_name'),
icon_button_editor(
'edit_queue_config_button',
'cog',
tooltip='Configure experiment queue generation'),
label='Generate Queue')
lgrp = VGroup(load_select, generate_queue)
ms_ed_grp = BorderVGroup(HGroup(
queue_factory_uitem(
'mass_spectrometer',
editor=myEnumEditor(
name=queue_factory_name('mass_spectrometers'))),
queue_factory_uitem(
'extract_device',
editor=myEnumEditor(
name=queue_factory_name('extract_devices')))),
lgrp,
queue_factory_item('default_lighting'),
label='Spectrometer/Extract Device')
name = queue_factory_name('available_conditionals')
queue_cond_grp = BorderHGroup(queue_factory_uitem(
'queue_conditionals_name',
label='Queue Conditionals',
editor=myEnumEditor(name=name)),
label='Queue Conditionals')
delay_grp = BorderVGroup(
queue_factory_item('delay_before_analyses',
label='Before Analyses (s)'),
queue_factory_item('delay_between_analyses',
label='Between Analyses (s)'),
queue_factory_item('delay_after_blank', label='After Blank (s)'),
queue_factory_item('delay_after_air', label='After Air (s)'),
label='Delays')
note_grp = BorderVGroup(queue_factory_uitem('note',
style='custom',
height=150),
label='Note')
queue_grp = VGroup(user_grp,
email_grp,
ms_ed_grp,
queue_cond_grp,
delay_grp,
note_grp,
label='Queue')
button_bar = HGroup(
save_button, add_button, clear_button, edit_button,
CustomLabel(run_factory_name('edit_mode_label'),
color='red',
width=40), spring)
button_bar2 = HGroup(
Item('auto_increment_id', label='Auto Increment L#'),
Item('auto_increment_position', label='Position'),
)
edit_grp = VFold(
queue_grp,
VGroup(self._get_info_group(),
self._get_extract_group(),
enabled_when=queue_factory_name('ok_make'),
label='General'), self._get_script_group(),
self._get_truncate_group())
v = View(VGroup(button_bar,
button_bar2,
UItem('pane.info_label', style='readonly'),
edit_grp,
enabled_when='edit_enabled'),
kind='live',
width=225)
return v