def get_run_fields(self):
"""Gets the QGroupBox that contains the fields for starting SuRVoS.
Returns:
PyQt5.QWidgets.GroupBox: GroupBox with run fields.
"""
self.run_button = QPushButton("Run SuRVoS")
advanced_button = QRadioButton("Advanced")
run_fields = QGroupBox("Run SuRVoS:")
run_layout = QGridLayout()
run_layout.addWidget(QLabel("Workspace Name:"), 0, 0)
workspaces = os.listdir(CHROOT)
self.workspaces_list = ComboBox()
for s in workspaces:
self.workspaces_list.addItem(key=s)
run_layout.addWidget(self.workspaces_list, 0, 0)
self.ws_name_linedt_2 = QLineEdit(self.workspace_config["workspace_name"])
self.ws_name_linedt_2.setAlignment(Qt.AlignLeft)
run_layout.addWidget(self.ws_name_linedt_2, 0, 2)
run_layout.addWidget(advanced_button, 1, 0)
run_layout.addWidget(self.adv_run_fields, 2, 1)
run_layout.addWidget(self.run_button, 3, 0, 1, 3)
run_fields.setLayout(run_layout)
advanced_button.toggled.connect(self.toggle_advanced)
self.run_button.clicked.connect(self.run_clicked)
return run_fields
def __init__(self, parent=None):
super(SVMWidget, self).__init__(parent=parent)
vbox = QtWidgets.QVBoxLayout()
vbox.setContentsMargins(0, 0, 0, 0)
self.setLayout(vbox)
self.type_combo = ComboBox()
self.type_combo.addCategory("Kernel Type:")
self.type_combo.addItem("linear")
self.type_combo.addItem("poly")
self.type_combo.addItem("rbf")
self.type_combo.addItem("sigmoid")
vbox.addWidget(self.type_combo)
self.penaltyc = LineEdit(default=1.0, parse=float)
self.gamma = LineEdit(default=1.0, parse=float)
vbox.addWidget(
HWidgets(
QtWidgets.QLabel("Penalty C:"),
self.penaltyc,
QtWidgets.QLabel("Gamma:"),
self.gamma,
stretch=[0, 1, 0, 1],
))
def __init__(self, parent=None):
super().__init__(parent=parent)
self.pipeline_combo = ComboBox()
self.vbox = VBox(self, spacing=4)
self.vbox.addWidget(self.pipeline_combo)
self.pipeline_combo.currentIndexChanged.connect(self.add_pipeline)
self.existing_pipelines = dict()
self._populate_pipelines()
def _add_model_type(self):
self.model_type = ComboBox()
self.model_type.addItem(key="unet3d")
self.model_type.addItem(key="fpn3d")
widget = HWidgets("Model type:",
self.model_type,
Spacing(35),
stretch=0)
self.add_row(widget)
def _add_projection_choice(self):
self.projection_type = ComboBox()
self.projection_type.addItem(key="None")
self.projection_type.addItem(key="pca")
self.projection_type.addItem(key="rbp")
self.projection_type.addItem(key="rproj")
self.projection_type.addItem(key="std")
widget = HWidgets("Projection:",
self.projection_type,
Spacing(35),
stretch=0)
self.add_row(widget)
def __init__(self, parent=None):
super(EnsembleWidget, self).__init__(parent=parent)
vbox = QtWidgets.QVBoxLayout()
vbox.setContentsMargins(0, 0, 0, 0)
self.setLayout(vbox)
self.type_combo = ComboBox()
self.type_combo.addCategory("Ensemble Type:")
self.type_combo.addItem("Random Forest")
self.type_combo.addItem("ExtraRandom Forest")
self.type_combo.addItem("AdaBoost")
self.type_combo.addItem("GradientBoosting")
#self.type_combo.addItem("XGBoost")
self.type_combo.currentIndexChanged.connect(self.on_ensemble_changed)
vbox.addWidget(self.type_combo)
self.ntrees = LineEdit(default=100, parse=int)
self.depth = LineEdit(default=15, parse=int)
self.lrate = LineEdit(default=1.0, parse=float)
self.subsample = LineEdit(default=1.0, parse=float)
vbox.addWidget(
HWidgets(
QtWidgets.QLabel("# Trees:"),
self.ntrees,
QtWidgets.QLabel("Max Depth:"),
self.depth,
stretch=[0, 1, 0, 1],
))
vbox.addWidget(
HWidgets(
QtWidgets.QLabel("Learn Rate:"),
self.lrate,
QtWidgets.QLabel("Subsample:"),
self.subsample,
stretch=[0, 1, 0, 1],
))
# self.btn_train_predict = PushButton('Train & Predict')
# self.btn_train_predict.clicked.connect(self.on_train_predict_clicked)
self.n_jobs = LineEdit(default=10, parse=int)
vbox.addWidget(HWidgets("Num Jobs", self.n_jobs))
def __init__(self, *args, **kwargs):
QtWidgets.QWidget.__init__(self, *args, **kwargs)
self.slice_mode = False
self.slider = Slider(value=0, vmax=cfg.slice_max - 1)
self.slider.setMinimumWidth(150)
self.slider.sliderReleased.connect(self._params_updated)
button_refresh = QPushButton("Refresh", self)
button_refresh.clicked.connect(self.button_refresh_clicked)
button_transfer = QPushButton("Transfer Layer")
button_transfer.clicked.connect(self.button_transfer_clicked)
self.button_slicemode = QPushButton("Slice mode", self)
self.button_slicemode.clicked.connect(self.button_slicemode_clicked)
workspaces = os.listdir(DataModel.g.CHROOT)
self.workspaces_list = ComboBox()
for s in workspaces:
self.workspaces_list.addItem(key=s)
workspaces_widget = HWidgets("Switch Workspaces:",
self.workspaces_list)
self.workspaces_list.setEditable(True)
self.workspaces_list.activated[str].connect(self.workspaces_selected)
self.hbox_layout0 = QtWidgets.QHBoxLayout()
hbox_layout_ws = QtWidgets.QHBoxLayout()
hbox_layout1 = QtWidgets.QHBoxLayout()
self.hbox_layout0.addWidget(self.slider)
self.slider.hide()
hbox_layout_ws.addWidget(workspaces_widget)
hbox_layout_ws.addWidget(button_refresh)
hbox_layout1.addWidget(button_transfer)
hbox_layout1.addWidget(self.button_slicemode)
vbox = VBox(self, margin=(1, 1, 1, 1), spacing=2)
vbox.addLayout(self.hbox_layout0)
vbox.addLayout(hbox_layout1)
vbox.addLayout(hbox_layout_ws)
def _add_classifier_choice(self):
self.classifier_type = ComboBox()
self.classifier_type.addItem(key="Ensemble")
self.classifier_type.addItem(key="SVM")
widget = HWidgets("Classifier:",
self.classifier_type,
Spacing(35),
stretch=0)
self.classifier_type.currentIndexChanged.connect(
self._on_classifier_changed)
self.clf_container = QtWidgets.QWidget()
clf_vbox = VBox(self, spacing=4)
clf_vbox.setContentsMargins(0, 0, 0, 0)
self.clf_container.setLayout(clf_vbox)
self.add_row(widget)
self.add_row(self.clf_container, max_height=500)
self.clf_container.layout().addWidget(self.ensembles)
def setup_annotation_widgets(self):
anno_group_box = QGroupBox("Annotations:")
anno_box_layout = QGridLayout()
# Labels
anno_box_layout.addWidget(QLabel("Annotation"), 0, 0, 1, 2)
anno_box_layout.addWidget(QLabel("File type"), 0, 2)
# Annotations combo
self.anno_source = AnnoComboBox()
anno_box_layout.addWidget(self.anno_source, 1, 0, 1, 2)
# File type combo
self.anno_ftype_combo = ComboBox()
self.add_filetypes_to_combo(self.anno_ftype_combo)
anno_box_layout.addWidget(self.anno_ftype_combo, 1, 2)
# Button
self.anno_export_btn = IconButton("fa.save",
"Export data",
accent=True)
self.anno_export_btn.clicked.connect(self.save_anno)
anno_box_layout.addWidget(self.anno_export_btn, 1, 3)
anno_group_box.setLayout(anno_box_layout)
return anno_group_box
def setup_feature_widgets(self):
feat_group_box = QGroupBox("Features:")
feat_box_layout = QGridLayout()
# Labels
feat_box_layout.addWidget(QLabel("Feature"), 0, 0, 1, 2)
feat_box_layout.addWidget(QLabel("File type"), 0, 2)
# Features combo
self.feat_source = FeatureComboBox()
feat_box_layout.addWidget(self.feat_source, 1, 0, 1, 2)
# File type combo
self.feat_ftype_combo = ComboBox()
self.add_filetypes_to_combo(self.feat_ftype_combo)
feat_box_layout.addWidget(self.feat_ftype_combo, 1, 2)
# Button
self.feat_export_btn = IconButton("fa.save",
"Export data",
accent=True)
self.feat_export_btn.clicked.connect(self.save_feature)
feat_box_layout.addWidget(self.feat_export_btn, 1, 3)
feat_group_box.setLayout(feat_box_layout)
return feat_group_box
def setup_pipeline_widgets(self):
pipe_group_box = QGroupBox("Pipeline output:")
pipe_box_layout = QGridLayout()
# Labels
pipe_box_layout.addWidget(QLabel("Pipeline"), 0, 0, 1, 2)
pipe_box_layout.addWidget(QLabel("File type"), 0, 2)
# Pipeline combo
self.pipe_source = SuperRegionSegmentComboBox()
pipe_box_layout.addWidget(self.pipe_source, 1, 0, 1, 2)
# File type combo
self.pipe_ftype_combo = ComboBox()
self.add_filetypes_to_combo(self.pipe_ftype_combo)
pipe_box_layout.addWidget(self.pipe_ftype_combo, 1, 2)
# Button
self.pipe_export_btn = IconButton("fa.save",
"Export data",
accent=True)
self.pipe_export_btn.clicked.connect(self.save_pipe)
pipe_box_layout.addWidget(self.pipe_export_btn, 1, 3)
pipe_group_box.setLayout(pipe_box_layout)
return pipe_group_box
class ButtonPanelWidget(QtWidgets.QWidget):
clientEvent = Signal(object)
def __init__(self, *args, **kwargs):
QtWidgets.QWidget.__init__(self, *args, **kwargs)
self.slice_mode = False
self.slider = Slider(value=0, vmax=cfg.slice_max - 1)
self.slider.setMinimumWidth(150)
self.slider.sliderReleased.connect(self._params_updated)
button_refresh = QPushButton("Refresh", self)
button_refresh.clicked.connect(self.button_refresh_clicked)
button_transfer = QPushButton("Transfer Layer")
button_transfer.clicked.connect(self.button_transfer_clicked)
self.button_slicemode = QPushButton("Slice mode", self)
self.button_slicemode.clicked.connect(self.button_slicemode_clicked)
workspaces = os.listdir(DataModel.g.CHROOT)
self.workspaces_list = ComboBox()
for s in workspaces:
self.workspaces_list.addItem(key=s)
workspaces_widget = HWidgets("Switch Workspaces:",
self.workspaces_list)
self.workspaces_list.setEditable(True)
self.workspaces_list.activated[str].connect(self.workspaces_selected)
self.hbox_layout0 = QtWidgets.QHBoxLayout()
hbox_layout_ws = QtWidgets.QHBoxLayout()
hbox_layout1 = QtWidgets.QHBoxLayout()
self.hbox_layout0.addWidget(self.slider)
self.slider.hide()
hbox_layout_ws.addWidget(workspaces_widget)
hbox_layout_ws.addWidget(button_refresh)
hbox_layout1.addWidget(button_transfer)
hbox_layout1.addWidget(self.button_slicemode)
vbox = VBox(self, margin=(1, 1, 1, 1), spacing=2)
vbox.addLayout(self.hbox_layout0)
vbox.addLayout(hbox_layout1)
vbox.addLayout(hbox_layout_ws)
def refresh_workspaces(self):
workspaces = os.listdir(DataModel.g.CHROOT)
self.workspaces_list.clear()
for s in workspaces:
self.workspaces_list.addItem(key=s)
self.slider.setMinimumWidth(cfg.base_dataset_shape[0])
def workspaces_selected(self):
selected_workspace = self.workspaces_list.value()
self.workspaces_list.blockSignals(True)
self.workspaces_list.select(selected_workspace)
self.workspaces_list.blockSignals(False)
cfg.ppw.clientEvent.emit({
"source": "panel_gui",
"data": "set_workspace",
"workspace": selected_workspace,
})
def sessions_selected(self):
cfg.ppw.clientEvent.emit({
"source": "panel_gui",
"data": "set_session",
"session": self.session_list.value(),
})
def button_setroi_clicked(self):
roi_start = self.roi_start.value()
roi_end = self.roi_end.value()
roi = [
roi_start[0],
roi_start[1],
roi_start[2],
roi_end[0],
roi_end[1],
roi_end[2],
]
self.refresh_workspaces()
cfg.ppw.clientEvent.emit({
"source": "panel_gui",
"data": "make_roi_ws",
"roi": roi
})
def button_refresh_clicked(self):
self.refresh_workspaces()
cfg.ppw.clientEvent.emit({
"source": "panel_gui",
"data": "empty_viewer",
"value": None
})
cfg.ppw.clientEvent.emit({
"source": "panel_gui",
"data": "refresh",
"value": None
})
def button_pause_save_clicked(self):
if cfg.pause_save:
self.button_pause_save.setText("Pause Saving to Server")
else:
self.button_pause_save.setText("Resume saving to Server")
cfg.pause_save = not cfg.pause_save
def button_transfer_clicked(self):
cfg.ppw.clientEvent.emit({
"source": "panel_gui",
"data": "transfer_layer",
"value": None
})
def button_slicemode_clicked(self):
if self.slice_mode:
self.slider.hide()
self.button_slicemode.setText("Slice Mode")
else:
logger.info(f"Slice mode {cfg.slice_max}")
self.slider.vmax = cfg.slice_max - 1
self.slider.setRange(0, cfg.slice_max - 1)
self.slider.show()
self.button_slicemode.setText("Volume Mode")
self.slice_mode = not self.slice_mode
cfg.ppw.clientEvent.emit({
"source": "button_slicemode",
"data": "slice_mode",
})
def _params_updated(self):
cfg.ppw.clientEvent.emit({
"source": "slider",
"data": "jump_to_slice",
"frame": self.slider.value()
})
class PipelinesPlugin(Plugin):
__icon__ = "fa.picture-o"
__pname__ = "pipelines"
__views__ = ["slice_viewer"]
__tab__ = "pipelines"
def __init__(self, parent=None):
super().__init__(parent=parent)
self.pipeline_combo = ComboBox()
self.vbox = VBox(self, spacing=4)
self.vbox.addWidget(self.pipeline_combo)
self.pipeline_combo.currentIndexChanged.connect(self.add_pipeline)
self.existing_pipelines = dict()
self._populate_pipelines()
def _populate_pipelines(self):
self.pipeline_params = {}
self.pipeline_combo.clear()
self.pipeline_combo.addItem("Add segmentation")
result = Launcher.g.run("pipelines", "available", workspace=True)
if not result:
params = {}
params["category"] = "superregion"
params["name"] = "s0"
params["type"] = "superregion_segment"
result = {}
result[0] = params
self.pipeline_params["superregion_segment"] = {
"sr_params": {
"type": "sr2",
}
}
else:
all_categories = sorted(set(p["category"] for p in result))
for i, category in enumerate(all_categories):
self.pipeline_combo.addItem(category)
self.pipeline_combo.model().item(i +
len(self.pipeline_params) +
1).setEnabled(False)
for f in [p for p in result if p["category"] == category]:
self.pipeline_params[f["name"]] = f["params"]
self.pipeline_combo.addItem(f["name"])
def add_pipeline(self, idx):
if idx <= 0:
return
if self.pipeline_combo.itemText(idx) == "":
return
logger.debug(f"Adding pipeline {self.pipeline_combo.itemText(idx)}")
pipeline_type = self.pipeline_combo.itemText(idx)
self.pipeline_combo.setCurrentIndex(0)
params = dict(pipeline_type=pipeline_type, workspace=True)
result = Launcher.g.run("pipelines", "create", **params)
if result:
fid = result["id"]
ftype = result["kind"]
fname = result["name"]
self._add_pipeline_widget(fid, ftype, fname, True)
_PipelineNotifier.notify()
def _add_pipeline_widget(self, fid, ftype, fname, expand=False):
widget = PipelineCard(fid, ftype, fname, self.pipeline_params[ftype])
widget.showContent(expand)
self.vbox.addWidget(widget)
self.existing_pipelines[fid] = widget
return widget
def clear(self):
for pipeline in list(self.existing_pipelines.keys()):
self.existing_pipelines.pop(pipeline).setParent(None)
self.existing_pipelines = {}
def setup(self):
self._populate_pipelines()
params = dict(workspace=DataModel.g.current_session + "@" +
DataModel.g.current_workspace)
result = Launcher.g.run("pipelines", "existing", **params)
logger.debug(f"Pipeline result {result}")
if result:
# Remove pipelines that no longer exist in the server
for pipeline in list(self.existing_pipelines.keys()):
if pipeline not in result:
self.existing_pipelines.pop(pipeline).setParent(None)
# Populate with new pipelines if any
for pipeline in sorted(result):
if pipeline in self.existing_pipelines:
continue
params = result[pipeline]
logger.debug(f"Pipeline params {params}")
fid = params.pop("id", pipeline)
ftype = params.pop("kind")
fname = params.pop("name", pipeline)
widget = self._add_pipeline_widget(fid, ftype, fname)
widget.update_params(params)
self.existing_pipelines[fid] = widget
class PipelineCard(Card):
def __init__(self, fid, ftype, fname, fparams, parent=None):
super().__init__(fname,
removable=True,
editable=True,
collapsible=True,
parent=parent)
self.pipeline_id = fid
self.pipeline_type = ftype
self.pipeline_name = fname
#from qtpy.QtWidgets import QProgressBar
#self.pbar = QProgressBar(self)
#self.add_row(self.pbar)
self.params = fparams
print(fparams)
self.widgets = dict()
if self.pipeline_type == "superregion_segment":
logger.debug("Adding a superregion_segment pipeline")
self._add_features_source()
self._add_annotations_source()
self._add_constrain_source()
self._add_regions_source()
self.ensembles = EnsembleWidget()
self.ensembles.train_predict.connect(self.compute_pipeline)
self.svm = SVMWidget()
self.svm.predict.connect(self.compute_pipeline)
self._add_classifier_choice()
self._add_projection_choice()
self._add_param("lam", type="FloatSlider", default=0.15)
self._add_confidence_choice()
elif self.pipeline_type == "rasterize_points":
self._add_annotations_source()
self._add_feature_source()
self._add_objects_source()
elif self.pipeline_type == "watershed":
self._add_annotations_source()
self._add_feature_source()
elif self.pipeline_type == "predict_segmentation_fcn":
self._add_annotations_source()
self._add_feature_source()
self._add_workflow_file()
self._add_model_type()
# self._add_patch_params()
elif self.pipeline_type == "label_postprocess":
self._add_annotations_source(label="Layer Over: ")
self._add_annotations_source2(label="Layer Base: ")
self.label_index = LineEdit(default=-1, parse=int)
#widget = HWidgets("Selected label:", self.label_index, Spacing(35), stretch=1)
#self.add_row(widget)
#self.offset = LineEdit(default=-1, parse=int)
#widget2 = HWidgets("Offset:", self.offset, Spacing(35), stretch=1)
#self.add_row(widget2)
elif self.pipeline_type == "cleaning":
# self._add_objects_source()
self._add_feature_source()
self._add_annotations_source()
elif self.pipeline_type == "train_2d_unet":
self._add_annotations_source()
self._add_feature_source()
self._add_unet_2d_training_params()
elif self.pipeline_type == "predict_2d_unet":
self._add_annotations_source()
self._add_feature_source()
self._add_unet_2d_prediction_params()
else:
logger.debug(f"Unsupported pipeline type {self.pipeline_type}.")
for pname, params in fparams.items():
if pname not in ["src", "dst"]:
self._add_param(pname, **params)
self._add_compute_btn()
self._add_view_btn()
def _add_model_type(self):
self.model_type = ComboBox()
self.model_type.addItem(key="unet3d")
self.model_type.addItem(key="fpn3d")
widget = HWidgets("Model type:",
self.model_type,
Spacing(35),
stretch=0)
self.add_row(widget)
def _add_patch_params(self):
self.patch_size = LineEdit3D(default=64, parse=int)
self.add_row(
HWidgets("Patch Size:", self.patch_size, Spacing(35), stretch=1))
def _add_unet_2d_training_params(self):
self.add_row(HWidgets("Training Parameters:", Spacing(35), stretch=1))
self.cycles_frozen = LineEdit(default=8, parse=int)
self.cycles_unfrozen = LineEdit(default=5, parse=int)
self.add_row(
HWidgets("No. Cycles Frozen:",
self.cycles_frozen,
"No. Cycles Unfrozen",
self.cycles_unfrozen,
stretch=1))
def _add_unet_2d_prediction_params(self):
self.model_file_line_edit = LineEdit(default="Filepath", parse=str)
model_input_btn = PushButton("Select Model", accent=True)
model_input_btn.clicked.connect(self.get_model_path)
self.radio_group = QtWidgets.QButtonGroup()
self.radio_group.setExclusive(True)
single_pp_rb = QRadioButton("Single plane")
single_pp_rb.setChecked(True)
self.radio_group.addButton(single_pp_rb, 1)
triple_pp_rb = QRadioButton("Three plane")
self.radio_group.addButton(triple_pp_rb, 3)
self.add_row(
HWidgets(self.model_file_line_edit, model_input_btn, Spacing(35)))
self.add_row(HWidgets("Prediction Parameters:", Spacing(35),
stretch=1))
self.add_row(HWidgets(single_pp_rb, triple_pp_rb, stretch=1))
def _add_workflow_file(self):
self.filewidget = FileWidget(extensions="*.pt", save=False)
self.add_row(self.filewidget)
self.filewidget.path_updated.connect(self.load_data)
def load_data(self, path):
self.model_fullname = path
print(f"Setting model fullname: {self.model_fullname}")
def _add_view_btn(self):
view_btn = PushButton("View", accent=True)
view_btn.clicked.connect(self.view_pipeline)
load_as_annotation_btn = PushButton("Load as annotation", accent=True)
load_as_annotation_btn.clicked.connect(self.load_as_annotation)
load_as_float_btn = PushButton("Load as image", accent=True)
load_as_float_btn.clicked.connect(self.load_as_float)
self.add_row(
HWidgets(None, load_as_float_btn, load_as_annotation_btn, view_btn,
Spacing(35)))
def _add_refine_choice(self):
self.refine_checkbox = CheckBox(checked=True)
self.add_row(
HWidgets("MRF Refinement:",
self.refine_checkbox,
Spacing(35),
stretch=0))
def _add_confidence_choice(self):
self.confidence_checkbox = CheckBox(checked=False)
self.add_row(
HWidgets("Confidence Map as Feature:",
self.confidence_checkbox,
Spacing(35),
stretch=0))
def _add_objects_source(self):
self.objects_source = ObjectComboBox(full=True)
self.objects_source.fill()
self.objects_source.setMaximumWidth(250)
widget = HWidgets("Objects:",
self.objects_source,
Spacing(35),
stretch=1)
self.add_row(widget)
def _add_classifier_choice(self):
self.classifier_type = ComboBox()
self.classifier_type.addItem(key="Ensemble")
self.classifier_type.addItem(key="SVM")
widget = HWidgets("Classifier:",
self.classifier_type,
Spacing(35),
stretch=0)
self.classifier_type.currentIndexChanged.connect(
self._on_classifier_changed)
self.clf_container = QtWidgets.QWidget()
clf_vbox = VBox(self, spacing=4)
clf_vbox.setContentsMargins(0, 0, 0, 0)
self.clf_container.setLayout(clf_vbox)
self.add_row(widget)
self.add_row(self.clf_container, max_height=500)
self.clf_container.layout().addWidget(self.ensembles)
def _on_classifier_changed(self, idx):
if idx == 0:
self.clf_container.layout().addWidget(self.ensembles)
self.svm.setParent(None)
elif idx == 1:
self.clf_container.layout().addWidget(self.svm)
self.ensembles.setParent(None)
def _add_projection_choice(self):
self.projection_type = ComboBox()
self.projection_type.addItem(key="None")
self.projection_type.addItem(key="pca")
self.projection_type.addItem(key="rbp")
self.projection_type.addItem(key="rproj")
self.projection_type.addItem(key="std")
widget = HWidgets("Projection:",
self.projection_type,
Spacing(35),
stretch=0)
self.add_row(widget)
def _add_feature_source(self):
self.feature_source = FeatureComboBox()
self.feature_source.fill()
self.feature_source.setMaximumWidth(250)
widget = HWidgets("Feature:",
self.feature_source,
Spacing(35),
stretch=1)
self.add_row(widget)
def _add_features_source(self):
self.features_source = MultiSourceComboBox()
self.features_source.fill()
self.features_source.setMaximumWidth(250)
cfg.pipelines_features_source = self.features_source
widget = HWidgets("Features:",
self.features_source,
Spacing(35),
stretch=1)
self.add_row(widget)
def _add_constrain_source(self):
print(self.annotations_source.value())
self.constrain_mask_source = AnnotationComboBox(header=(None, "None"),
full=True)
self.constrain_mask_source.fill()
self.constrain_mask_source.setMaximumWidth(250)
widget = HWidgets("Constrain mask:",
self.constrain_mask_source,
Spacing(35),
stretch=1)
self.add_row(widget)
def _add_annotations_source(self, label="Annotation"):
self.annotations_source = LevelComboBox(full=True)
self.annotations_source.fill()
self.annotations_source.setMaximumWidth(250)
widget = HWidgets(label,
self.annotations_source,
Spacing(35),
stretch=1)
self.add_row(widget)
def _add_annotations_source2(self, label="Annotation 2"):
self.annotations_source2 = LevelComboBox(full=True)
self.annotations_source2.fill()
self.annotations_source2.setMaximumWidth(250)
widget = HWidgets(label,
self.annotations_source2,
Spacing(35),
stretch=1)
self.add_row(widget)
def _add_pipelines_source(self):
self.pipelines_source = PipelinesComboBox()
self.pipelines_source.fill()
self.pipelines_source.setMaximumWidth(250)
widget = HWidgets("Segmentation:",
self.pipelines_source,
Spacing(35),
stretch=1)
self.add_row(widget)
def _add_regions_source(self):
self.regions_source = RegionComboBox(full=True) # SourceComboBox()
self.regions_source.fill()
self.regions_source.setMaximumWidth(250)
widget = HWidgets("Superregions:",
self.regions_source,
Spacing(35),
stretch=1)
cfg.pipelines_regions_source = self.regions_source
self.add_row(widget)
def _add_param(self, name, title=None, type="String", default=None):
if type == "Int":
p = LineEdit(default=0, parse=int)
elif type == "FloatSlider":
p = RealSlider(value=0.0, vmax=1, vmin=0)
title = "MRF Refinement Amount:"
elif type == "Float":
p = LineEdit(default=0.0, parse=float)
title = title
elif type == "FloatOrVector":
p = LineEdit3D(default=0, parse=float)
elif type == "IntOrVector":
p = LineEdit3D(default=0, parse=int)
elif type == "SmartBoolean":
p = CheckBox(checked=True)
else:
p = None
if title is None:
title = name
if p:
self.widgets[name] = p
self.add_row(HWidgets(None, title, p, Spacing(35)))
def _add_compute_btn(self):
compute_btn = PushButton("Compute", accent=True)
compute_btn.clicked.connect(self.compute_pipeline)
self.add_row(HWidgets(None, compute_btn, Spacing(35)))
def update_params(self, params):
logger.debug(f"Pipeline update params {params}")
for k, v in params.items():
if k in self.widgets:
self.widgets[k].setValue(v)
if "anno_id" in params:
if params["anno_id"] is not None:
self.annotations_source.select(
os.path.join("annotations/", params["anno_id"]))
if "object_id" in params:
if params["object_id"] is not None:
self.objects_source.select(
os.path.join("objects/", params["object_id"]))
if "feature_id" in params:
for source in params["feature_id"]:
self.feature_source.select(os.path.join("features/", source))
if "feature_ids" in params:
for source in params["feature_ids"]:
self.features_source.select(os.path.join("features/", source))
if "region_id" in params:
if params["region_id"] is not None:
self.regions_source.select(
os.path.join("regions/", params["region_id"]))
if "constrain_mask" in params:
if (params["constrain_mask"] is not None
and params["constrain_mask"] != "None"):
import ast
constrain_mask_dict = ast.literal_eval(
params["constrain_mask"])
print(constrain_mask_dict)
constrain_mask_source = (constrain_mask_dict["level"] + ":" +
str(constrain_mask_dict["idx"]))
print(f"Constrain mask source {constrain_mask_source}")
self.constrain_mask_source.select(constrain_mask_source)
def card_deleted(self):
params = dict(pipeline_id=self.pipeline_id, workspace=True)
result = Launcher.g.run("pipelines", "remove", **params)
if result["done"]:
self.setParent(None)
_PipelineNotifier.notify()
cfg.ppw.clientEvent.emit({
"source": "pipelines",
"data": "remove_layer",
"layer_name": self.pipeline_id,
})
def view_pipeline(self):
logger.debug(f"View pipeline_id {self.pipeline_id}")
with progress(total=2) as pbar:
pbar.set_description("Viewing feature")
pbar.update(1)
if self.annotations_source:
if self.annotations_source.value():
level_id = str(self.annotations_source.value().rsplit(
"/", 1)[-1])
else:
level_id = '001_level'
logger.debug(f"Assigning annotation level {level_id}")
cfg.ppw.clientEvent.emit({
"source": "pipelines",
"data": "view_pipeline",
"pipeline_id": self.pipeline_id,
"level_id": level_id,
})
pbar.update(1)
def get_model_path(self):
workspace_path = os.path.join(DataModel.g.CHROOT,
DataModel.g.current_workspace)
self.model_path, _ = QtWidgets.QFileDialog.getOpenFileName(
self, ("Select model"), workspace_path, ("Model files (*.zip)"))
self.model_file_line_edit.setValue(self.model_path)
def load_as_float(self):
logger.debug(f"Loading prediction {self.pipeline_id} as float image.")
# get pipeline output
src = DataModel.g.dataset_uri(self.pipeline_id, group="pipelines")
with DatasetManager(src, out=None, dtype="uint32", fillvalue=0) as DM:
src_arr = DM.sources[0][:]
# create new float image
params = dict(feature_type="raw", workspace=True)
result = Launcher.g.run("features", "create", **params)
if result:
fid = result["id"]
ftype = result["kind"]
fname = result["name"]
logger.debug(
f"Created new object in workspace {fid}, {ftype}, {fname}")
dst = DataModel.g.dataset_uri(fid, group="features")
with DatasetManager(dst, out=dst, dtype="float32",
fillvalue=0) as DM:
DM.out[:] = src_arr
cfg.ppw.clientEvent.emit({
"source": "workspace_gui",
"data": "refresh",
"value": None
})
def load_as_annotation(self):
logger.debug(f"Loading prediction {self.pipeline_id} as annotation.")
# get pipeline output
src = DataModel.g.dataset_uri(self.pipeline_id, group="pipelines")
with DatasetManager(src, out=None, dtype="uint32", fillvalue=0) as DM:
src_arr = DM.sources[0][:]
label_values = np.unique(src_arr)
# create new level
params = dict(level=self.pipeline_id, workspace=True)
result = Launcher.g.run("annotations", "add_level", workspace=True)
# create a blank label for each unique value in the pipeline output array
if result:
level_id = result["id"]
for v in label_values:
params = dict(
level=level_id,
idx=int(v),
name=str(v),
color="#11FF11",
workspace=True,
)
label_result = Launcher.g.run("annotations", "add_label",
**params)
params = dict(
level=str(self.annotations_source.value().rsplit("/", 1)[-1]),
workspace=True,
)
anno_result = Launcher.g.run("annotations", "get_levels",
**params)[0]
params = dict(level=str(level_id), workspace=True)
level_result = Launcher.g.run("annotations", "get_levels",
**params)[0]
try:
# set the new level color mapping to the mapping from the pipeline
for v in level_result["labels"].keys():
if v in anno_result["labels"]:
label_hex = anno_result["labels"][v]["color"]
label = dict(
idx=int(v),
name=str(v),
color=label_hex,
)
params = dict(level=result["id"], workspace=True)
label_result = Launcher.g.run("annotations",
"update_label", **params,
**label)
except Exception as err:
logger.debug(f"Exception {err}")
fid = result["id"]
ftype = result["kind"]
fname = result["name"]
logger.debug(
f"Created new object in workspace {fid}, {ftype}, {fname}")
# set levels array to pipeline output array
dst = DataModel.g.dataset_uri(fid, group="annotations")
with DatasetManager(dst, out=dst, dtype="uint32",
fillvalue=0) as DM:
DM.out[:] = src_arr
cfg.ppw.clientEvent.emit({
"source": "workspace_gui",
"data": "refresh",
"value": None
})
def setup_params_superregion_segment(self, dst):
feature_names_list = [
n.rsplit("/", 1)[-1] for n in self.features_source.value()
]
src_grp = None if self.annotations_source.currentIndex(
) == 0 else "pipelines"
src = DataModel.g.dataset_uri(
self.annotations_source.value().rsplit("/", 1)[-1],
group="annotations",
)
all_params = dict(src=src, modal=True)
all_params["workspace"] = DataModel.g.current_workspace
logger.info(f"Setting src to {self.annotations_source.value()} ")
all_params["region_id"] = str(self.regions_source.value().rsplit(
"/", 1)[-1])
all_params["feature_ids"] = feature_names_list
all_params["anno_id"] = str(self.annotations_source.value().rsplit(
"/", 1)[-1])
if self.constrain_mask_source.value() != None:
all_params["constrain_mask"] = self.constrain_mask_source.value(
) # .rsplit("/", 1)[-1]
else:
all_params["constrain_mask"] = "None"
all_params["dst"] = dst
all_params["refine"] = self.widgets["refine"].value()
all_params["lam"] = self.widgets["lam"].value()
all_params["classifier_type"] = self.classifier_type.value()
all_params["projection_type"] = self.projection_type.value()
all_params["confidence"] = self.confidence_checkbox.value()
if self.classifier_type.value() == "Ensemble":
all_params["classifier_params"] = self.ensembles.get_params()
else:
all_params["classifier_params"] = self.svm.get_params()
return all_params
def setup_params_rasterize_points(self, dst):
src = DataModel.g.dataset_uri(self.feature_source.value(),
group="features")
all_params = dict(src=src, modal=True)
all_params["workspace"] = DataModel.g.current_workspace
# all_params["anno_id"] = str(
# self.annotations_source.value().rsplit("/", 1)[-1]
# )
all_params["feature_id"] = self.feature_source.value()
all_params["object_id"] = str(self.objects_source.value())
all_params["acwe"] = self.widgets["acwe"].value()
# all_params["object_scale"] = self.widgets["object_scale"].value()
# all_params["object_offset"] = self.widgets["object_offset"].value()
all_params["dst"] = dst
return all_params
def setup_params_watershed(self, dst):
src = DataModel.g.dataset_uri(self.feature_source.value(),
group="features")
all_params = dict(src=src, dst=dst, modal=True)
all_params["workspace"] = DataModel.g.current_workspace
all_params["dst"] = self.pipeline_id
all_params["anno_id"] = str(self.annotations_source.value().rsplit(
"/", 1)[-1])
return all_params
def setup_params_predict_segmentation_fcn(self, dst):
src = DataModel.g.dataset_uri(self.feature_source.value(),
group="features")
all_params = dict(src=src, dst=dst, modal=True)
all_params["workspace"] = DataModel.g.current_workspace
all_params["anno_id"] = str(self.annotations_source.value().rsplit(
"/", 1)[-1])
all_params["feature_id"] = self.feature_source.value()
all_params["model_fullname"] = self.model_fullname
all_params["model_type"] = self.model_type.value()
all_params["dst"] = self.pipeline_id
return all_params
def setup_params_label_postprocess(self, dst):
all_params = dict(modal=True)
all_params["workspace"] = DataModel.g.current_workspace
print(self.annotations_source.value())
if (self.annotations_source.value()):
all_params["level_over"] = str(
self.annotations_source.value().rsplit("/", 1)[-1])
else:
all_params["level_over"] = "None"
all_params["level_base"] = str(self.annotations_source2.value().rsplit(
"/", 1)[-1])
all_params["dst"] = dst
#all_params["selected_label"] = int(self.label_index.value())
#all_params["offset"] = int(self.offset.value())
all_params["selected_label"] = int(
self.widgets["selected_label"].value())
all_params["offset"] = int(self.widgets["offset"].value())
return all_params
def setup_params_cleaning(self, dst):
all_params = dict(dst=dst, modal=True)
all_params["workspace"] = DataModel.g.current_workspace
all_params["feature_id"] = str(self.feature_source.value())
# all_params["object_id"] = str(self.objects_source.value())
return all_params
def setup_params_train_2d_unet(self, dst):
src = DataModel.g.dataset_uri(self.feature_source.value(),
group="features")
all_params = dict(src=src, dst=dst, modal=True)
all_params["workspace"] = DataModel.g.current_workspace
all_params["feature_id"] = str(self.feature_source.value())
all_params["anno_id"] = str(self.annotations_source.value().rsplit(
"/", 1)[-1])
all_params["unet_train_params"] = dict(
cyc_frozen=self.cycles_frozen.value(),
cyc_unfrozen=self.cycles_unfrozen.value())
return all_params
def setup_params_predict_2d_unet(self, dst):
src = DataModel.g.dataset_uri(self.feature_source.value(),
group="features")
all_params = dict(src=src, dst=dst, modal=True)
all_params["workspace"] = DataModel.g.current_workspace
all_params["feature_id"] = str(self.feature_source.value())
all_params["anno_id"] = str(self.annotations_source.value().rsplit(
"/", 1)[-1])
all_params["model_path"] = str(self.model_file_line_edit.value())
all_params["no_of_planes"] = self.radio_group.checkedId()
return all_params
def compute_pipeline(self):
dst = DataModel.g.dataset_uri(self.pipeline_id, group="pipelines")
with progress(total=3) as pbar:
pbar.set_description("Calculating pipeline")
pbar.update(1)
try:
if self.pipeline_type == "superregion_segment":
all_params = self.setup_params_superregion_segment(dst)
elif self.pipeline_type == "rasterize_points":
all_params = self.setup_params_rasterize_points(dst)
elif self.pipeline_type == "watershed":
all_params = self.setup_params_watershed(dst)
elif self.pipeline_type == "predict_segmentation_fcn":
all_params = self.setup_params_predict_segmentation_fcn(
dst)
elif self.pipeline_type == "label_postprocess":
all_params = self.setup_params_label_postprocess(dst)
elif self.pipeline_type == "cleaning":
all_params = self.setup_params_cleaning(dst)
elif self.pipeline_type == "train_2d_unet":
all_params = self.setup_params_train_2d_unet(dst)
elif self.pipeline_type == "predict_2d_unet":
all_params = self.setup_params_predict_2d_unet(dst)
else:
logger.warning(
f"No action exists for pipeline: {self.pipeline_type}")
all_params.update(
{k: v.value()
for k, v in self.widgets.items()})
logger.info(
f"Computing pipelines {self.pipeline_type} {all_params}")
try:
pbar.update(1)
result = Launcher.g.run("pipelines", self.pipeline_type,
**all_params)
print(result)
except Exception as err:
print(err)
if result is not None:
pbar.update(1)
except Exception as e:
print(e)
def card_title_edited(self, newtitle):
params = dict(pipeline_id=self.pipeline_id,
new_name=newtitle,
workspace=True)
result = Launcher.g.run("pipelines", "rename", **params)
if result["done"]:
_PipelineNotifier.notify()
return result["done"]
class EnsembleWidget(QtWidgets.QWidget):
train_predict = Signal(dict)
def __init__(self, parent=None):
super(EnsembleWidget, self).__init__(parent=parent)
vbox = QtWidgets.QVBoxLayout()
vbox.setContentsMargins(0, 0, 0, 0)
self.setLayout(vbox)
self.type_combo = ComboBox()
self.type_combo.addCategory("Ensemble Type:")
self.type_combo.addItem("Random Forest")
self.type_combo.addItem("ExtraRandom Forest")
self.type_combo.addItem("AdaBoost")
self.type_combo.addItem("GradientBoosting")
#self.type_combo.addItem("XGBoost")
self.type_combo.currentIndexChanged.connect(self.on_ensemble_changed)
vbox.addWidget(self.type_combo)
self.ntrees = LineEdit(default=100, parse=int)
self.depth = LineEdit(default=15, parse=int)
self.lrate = LineEdit(default=1.0, parse=float)
self.subsample = LineEdit(default=1.0, parse=float)
vbox.addWidget(
HWidgets(
QtWidgets.QLabel("# Trees:"),
self.ntrees,
QtWidgets.QLabel("Max Depth:"),
self.depth,
stretch=[0, 1, 0, 1],
))
vbox.addWidget(
HWidgets(
QtWidgets.QLabel("Learn Rate:"),
self.lrate,
QtWidgets.QLabel("Subsample:"),
self.subsample,
stretch=[0, 1, 0, 1],
))
# self.btn_train_predict = PushButton('Train & Predict')
# self.btn_train_predict.clicked.connect(self.on_train_predict_clicked)
self.n_jobs = LineEdit(default=10, parse=int)
vbox.addWidget(HWidgets("Num Jobs", self.n_jobs))
def on_ensemble_changed(self, idx):
if idx == 2:
self.ntrees.setDefault(50)
else:
self.ntrees.setDefault(100)
if idx == 3:
self.lrate.setDefault(0.1)
self.depth.setDefault(3)
else:
self.lrate.setDefault(1.0)
self.depth.setDefault(15)
def on_train_predict_clicked(self):
ttype = ["rf", "erf", "ada", "gbf", "xgb"]
params = {
"clf": "ensemble",
"type": ttype[self.type_combo.currentIndex()],
"n_estimators": self.ntrees.value(),
"max_depth": self.depth.value(),
"learning_rate": self.lrate.value(),
"subsample": self.subsample.value(),
"n_jobs": self.n_jobs.value(),
}
self.train_predict.emit(params)
def get_params(self):
ttype = ["rf", "erf", "ada", "gbf", "xgb"]
if self.type_combo.currentIndex() - 1 == 0:
current_index = 0
else:
current_index = self.type_combo.currentIndex() - 1
logger.debug(f"Ensemble type_combo index: {current_index}")
params = {
"clf": "ensemble",
"type": ttype[current_index],
"n_estimators": self.ntrees.value(),
"max_depth": self.depth.value(),
"learning_rate": self.lrate.value(),
"subsample": self.subsample.value(),
"n_jobs": self.n_jobs.value(),
}
return params
class SVMWidget(QtWidgets.QWidget):
predict = Signal(dict)
def __init__(self, parent=None):
super(SVMWidget, self).__init__(parent=parent)
vbox = QtWidgets.QVBoxLayout()
vbox.setContentsMargins(0, 0, 0, 0)
self.setLayout(vbox)
self.type_combo = ComboBox()
self.type_combo.addCategory("Kernel Type:")
self.type_combo.addItem("linear")
self.type_combo.addItem("poly")
self.type_combo.addItem("rbf")
self.type_combo.addItem("sigmoid")
vbox.addWidget(self.type_combo)
self.penaltyc = LineEdit(default=1.0, parse=float)
self.gamma = LineEdit(default=1.0, parse=float)
vbox.addWidget(
HWidgets(
QtWidgets.QLabel("Penalty C:"),
self.penaltyc,
QtWidgets.QLabel("Gamma:"),
self.gamma,
stretch=[0, 1, 0, 1],
))
def on_predict_clicked(self):
params = {
"clf": "svm",
"kernel": self.type_combo.currentText(),
"C": self.penaltyc.value(),
"gamma": self.gamma.value(),
}
self.predict.emit(params)
def get_params(self):
params = {
"clf": "svm",
"kernel": self.type_combo.currentText(),
"C": self.penaltyc.value(),
"gamma": self.gamma.value(),
"type": self.type_combo.value(),
}
return params
class ServerPlugin(Plugin):
__icon__ = "fa.qrcode"
__pname__ = "server"
__views__ = ["slice_viewer"]
__tab__ = "server"
def __init__(self, parent=None):
super().__init__(parent=parent)
run_config = {
"server_ip": "127.0.0.1",
"server_port": "8134",
"workspace_name": "test_hunt_d4b",
"use_ssh": False,
"ssh_host": "ws168.diamond.ac.uk",
"ssh_port": "22",
}
workspace_config = {
"dataset_name": "data",
"datasets_dir": "/path/to/my/data/dir",
"vol_fname": "myfile.h5",
"workspace_name": "my_survos_workspace",
"downsample_by": "1",
}
from survos2.server.config import cfg
pipeline_config = dict(cfg)
self.run_config = run_config
self.workspace_config = workspace_config
self.pipeline_config = pipeline_config
self.server_process = None
self.client_process = None
self.layout = QVBoxLayout()
tabwidget = QTabWidget()
tab1 = QWidget()
tab2 = QWidget()
tabwidget.addTab(tab1, "Setup and Start Survos")
self.create_workspace_button = QPushButton("Create workspace")
tab1.layout = QVBoxLayout()
tab1.setLayout(tab1.layout)
chroot_fields = self.get_chroot_fields()
tab1.layout.addWidget(chroot_fields)
workspace_fields = self.get_workspace_fields()
tab1.layout.addWidget(workspace_fields)
self.setup_adv_run_fields()
self.adv_run_fields.hide()
run_fields = self.get_run_fields()
tab1.layout.addWidget(run_fields)
output_config_button = QPushButton("Save config")
self.create_workspace_button.clicked.connect(
self.create_workspace_clicked)
output_config_button.clicked.connect(self.output_config_clicked)
self.layout.addWidget(tabwidget)
self.setGeometry(300, 300, 600, 400)
self.setWindowTitle("SuRVoS Settings Editor")
current_fpth = os.path.dirname(os.path.abspath(__file__))
self.setWindowIcon(
QIcon(os.path.join(current_fpth, "resources", "logo.png")))
self.setLayout(self.layout)
self.show()
def get_chroot_fields(self):
chroot_fields = QGroupBox("Set Main Directory for Storing Workspaces:")
chroot_fields.setMaximumHeight(130)
chroot_layout = QGridLayout()
self.given_chroot_linedt = QLineEdit(CHROOT)
chroot_layout.addWidget(self.given_chroot_linedt, 1, 0, 1, 2)
set_chroot_button = QPushButton("Set Workspaces Root")
chroot_layout.addWidget(set_chroot_button, 1, 2)
chroot_fields.setLayout(chroot_layout)
set_chroot_button.clicked.connect(self.set_chroot)
return chroot_fields
def get_workspace_fields(self):
"""Gets the QGroupBox that contains all the fields for setting up the workspace.
Returns:
PyQt5.QWidgets.GroupBox: GroupBox with workspace fields.
"""
select_data_button = QPushButton("Select")
workspace_fields = QGroupBox("Create New Workspace:")
wf_layout = QGridLayout()
wf_layout.addWidget(QLabel("Data File Path:"), 0, 0)
current_data_path = Path(self.workspace_config["datasets_dir"],
self.workspace_config["vol_fname"])
self.data_filepth_linedt = QLineEdit(str(current_data_path))
wf_layout.addWidget(self.data_filepth_linedt, 1, 0, 1, 2)
wf_layout.addWidget(select_data_button, 1, 2)
wf_layout.addWidget(QLabel("HDF5 Internal Data Path:"), 2, 0, 1, 1)
ws_dataset_name = self.workspace_config["dataset_name"]
internal_h5_path = (ws_dataset_name
if str(ws_dataset_name).startswith("/") else "/" +
ws_dataset_name)
self.h5_intpth_linedt = QLineEdit(internal_h5_path)
wf_layout.addWidget(self.h5_intpth_linedt, 2, 1, 1, 1)
wf_layout.addWidget(QLabel("Workspace Name:"), 3, 0)
self.ws_name_linedt_1 = QLineEdit(
self.workspace_config["workspace_name"])
wf_layout.addWidget(self.ws_name_linedt_1, 3, 1)
wf_layout.addWidget(QLabel("Downsample Factor:"), 4, 0)
self.downsample_spinner = QSpinBox()
self.downsample_spinner.setRange(1, 10)
self.downsample_spinner.setSpecialValueText("None")
self.downsample_spinner.setMaximumWidth(60)
self.downsample_spinner.setValue(
int(self.workspace_config["downsample_by"]))
wf_layout.addWidget(self.downsample_spinner, 4, 1, 1, 1)
# ROI
self.setup_roi_fields()
wf_layout.addWidget(self.roi_fields, 4, 2, 1, 2)
self.roi_fields.hide()
wf_layout.addWidget(self.create_workspace_button, 5, 0, 1, 3)
workspace_fields.setLayout(wf_layout)
select_data_button.clicked.connect(self.launch_data_loader)
return workspace_fields
def setup_roi_fields(self):
"""Sets up the QGroupBox that displays the ROI dimensions, if selected."""
self.roi_fields = QGroupBox("ROI:")
roi_fields_layout = QHBoxLayout()
# z
roi_fields_layout.addWidget(QLabel("z:"), 0)
self.zstart_roi_val = QLabel("0")
roi_fields_layout.addWidget(self.zstart_roi_val, 1)
roi_fields_layout.addWidget(QLabel("-"), 2)
self.zend_roi_val = QLabel("0")
roi_fields_layout.addWidget(self.zend_roi_val, 3)
# y
roi_fields_layout.addWidget(QLabel("y:"), 4)
self.ystart_roi_val = QLabel("0")
roi_fields_layout.addWidget(self.ystart_roi_val, 5)
roi_fields_layout.addWidget(QLabel("-"), 6)
self.yend_roi_val = QLabel("0")
roi_fields_layout.addWidget(self.yend_roi_val, 7)
# x
roi_fields_layout.addWidget(QLabel("x:"), 8)
self.xstart_roi_val = QLabel("0")
roi_fields_layout.addWidget(self.xstart_roi_val, 9)
roi_fields_layout.addWidget(QLabel("-"), 10)
self.xend_roi_val = QLabel("0")
roi_fields_layout.addWidget(self.xend_roi_val, 11)
self.roi_fields.setLayout(roi_fields_layout)
def setup_adv_run_fields(self):
"""Sets up the QGroupBox that displays the advanced optiona for starting SuRVoS2."""
self.adv_run_fields = QGroupBox("Advanced Run Settings:")
adv_run_layout = QGridLayout()
adv_run_layout.addWidget(QLabel("Server IP Address:"), 0, 0)
self.server_ip_linedt = QLineEdit(self.run_config["server_ip"])
adv_run_layout.addWidget(self.server_ip_linedt, 0, 1)
adv_run_layout.addWidget(QLabel("Server Port:"), 1, 0)
self.server_port_linedt = QLineEdit(self.run_config["server_port"])
adv_run_layout.addWidget(self.server_port_linedt, 1, 1)
# SSH Info
self.ssh_button = QRadioButton("Use SSH")
self.ssh_button.setAutoExclusive(False)
adv_run_layout.addWidget(self.ssh_button, 0, 2)
ssh_flag = self.run_config.get("use_ssh", False)
if ssh_flag:
self.ssh_button.setChecked(True)
self.ssh_button.toggled.connect(self.toggle_ssh)
self.adv_ssh_fields = QGroupBox("SSH Settings:")
adv_ssh_layout = QGridLayout()
adv_ssh_layout.setColumnStretch(2, 2)
ssh_host_label = QLabel("Host")
self.ssh_host_linedt = QLineEdit(self.run_config.get("ssh_host", ""))
adv_ssh_layout.addWidget(ssh_host_label, 0, 0)
adv_ssh_layout.addWidget(self.ssh_host_linedt, 0, 1, 1, 2)
ssh_user_label = QLabel("Username")
self.ssh_username_linedt = QLineEdit(self.get_login_username())
adv_ssh_layout.addWidget(ssh_user_label, 1, 0)
adv_ssh_layout.addWidget(self.ssh_username_linedt, 1, 1, 1, 2)
ssh_port_label = QLabel("Port")
self.ssh_port_linedt = QLineEdit(self.run_config.get("ssh_port", ""))
adv_ssh_layout.addWidget(ssh_port_label, 2, 0)
adv_ssh_layout.addWidget(self.ssh_port_linedt, 2, 1, 1, 2)
self.adv_ssh_fields.setLayout(adv_ssh_layout)
#adv_run_layout.addWidget(self.adv_ssh_fields, 1, 2, 2, 5)
self.adv_run_fields.setLayout(adv_run_layout)
def get_run_fields(self):
"""Gets the QGroupBox that contains the fields for starting SuRVoS.
Returns:
PyQt5.QWidgets.GroupBox: GroupBox with run fields.
"""
self.run_button = QPushButton("Start Server")
self.stop_button = QPushButton("Stop Server")
self.existing_button = QPushButton("Use Existing Server")
advanced_button = QRadioButton("Advanced")
run_fields = QGroupBox("Run SuRVoS:")
run_layout = QGridLayout()
workspaces = os.listdir(CHROOT)
self.workspaces_list = ComboBox()
for s in workspaces:
self.workspaces_list.addItem(key=s)
run_layout.addWidget(QLabel("Workspace Name:"), 0, 0)
self.ws_name_linedt_2 = QLineEdit(
self.workspace_config["workspace_name"])
self.ws_name_linedt_2.setAlignment(Qt.AlignLeft)
self.workspaces_list.setLineEdit(self.ws_name_linedt_2)
# run_layout.addWidget(self.ws_name_linedt_2, 0, 1)
run_layout.addWidget(self.workspaces_list, 0, 1)
run_layout.addWidget(advanced_button, 1, 0)
run_layout.addWidget(self.adv_run_fields, 2, 1)
run_layout.addWidget(self.run_button, 3, 0, 1, 3)
run_layout.addWidget(self.stop_button, 4, 0, 1, 3)
run_layout.addWidget(self.existing_button, 5, 0, 1, 3)
run_fields.setLayout(run_layout)
advanced_button.toggled.connect(self.toggle_advanced)
self.run_button.clicked.connect(self.run_clicked)
self.stop_button.clicked.connect(self.stop_clicked)
self.existing_button.clicked.connect(self.existing_clicked)
return run_fields
def get_login_username(self):
try:
user = getpass.getuser()
except Exception:
user = ""
return user
def refresh_chroot(self):
workspaces = os.listdir(DataModel.g.CHROOT)
self.workspaces_list.clear()
for s in workspaces:
self.workspaces_list.addItem(key=s)
@pyqtSlot()
def set_chroot(self):
CHROOT = self.given_chroot_linedt.text()
Config.update({"model": {"chroot": CHROOT}})
logger.debug(f"Setting CHROOT to {CHROOT}")
DataModel.g.CHROOT = CHROOT
self.refresh_chroot()
@pyqtSlot()
def launch_data_loader(self):
"""Load the dialog box widget to select data with data preview window and ROI selection."""
path = None
int_h5_pth = None
dialog = LoadDataDialog(self)
result = dialog.exec_()
self.roi_limits = None
if result == QDialog.Accepted:
path = dialog.winput.path.text()
int_h5_pth = dialog.int_h5_pth.text()
down_factor = dialog.downsample_spinner.value()
if path and int_h5_pth:
self.data_filepth_linedt.setText(path)
self.h5_intpth_linedt.setText(int_h5_pth)
self.downsample_spinner.setValue(down_factor)
if dialog.roi_changed:
self.roi_limits = tuple(map(str, dialog.get_roi_limits()))
self.roi_fields.show()
self.update_roi_fields_from_dialog()
else:
self.roi_fields.hide()
def update_roi_fields_from_dialog(self):
"""Updates the ROI fields in the main window."""
x_start, x_end, y_start, y_end, z_start, z_end = self.roi_limits
self.xstart_roi_val.setText(x_start)
self.xend_roi_val.setText(x_end)
self.ystart_roi_val.setText(y_start)
self.yend_roi_val.setText(y_end)
self.zstart_roi_val.setText(z_start)
self.zend_roi_val.setText(z_end)
@pyqtSlot()
def toggle_advanced(self):
"""Controls displaying/hiding the advanced run fields on radio button toggle."""
rbutton = self.sender()
if rbutton.isChecked():
self.adv_run_fields.show()
else:
self.adv_run_fields.hide()
@pyqtSlot()
def toggle_ssh(self):
"""Controls displaying/hiding the SSH fields on radio button toggle."""
rbutton = self.sender()
if rbutton.isChecked():
self.adv_ssh_fields.show()
else:
self.adv_ssh_fields.hide()
@pyqtSlot()
def create_workspace_clicked(self):
"""Performs checks and coordinates workspace creation on button press."""
logger.debug("Creating workspace: ")
# Set the path to the data file
vol_path = Path(self.data_filepth_linedt.text())
if not vol_path.is_file():
err_str = f"No data file exists at {vol_path}!"
logger.error(err_str)
self.button_feedback_response(err_str,
self.create_workspace_button,
"maroon")
else:
self.workspace_config["datasets_dir"] = str(vol_path.parent)
self.workspace_config["vol_fname"] = str(vol_path.name)
dataset_name = self.h5_intpth_linedt.text()
self.workspace_config["dataset_name"] = str(dataset_name).strip(
"/")
# Set the workspace name
ws_name = self.ws_name_linedt_1.text()
self.workspace_config["workspace_name"] = ws_name
# Set the downsample factor
ds_factor = self.downsample_spinner.value()
self.workspace_config["downsample_by"] = ds_factor
# Set the ROI limits if they exist
if self.roi_limits:
self.workspace_config["roi_limits"] = self.roi_limits
try:
response = init_ws(self.workspace_config)
_, error = response
if not error:
self.button_feedback_response(
"Workspace created sucessfully",
self.create_workspace_button,
"green",
)
# Update the workspace name in the 'Run' section
self.ws_name_linedt_2.setText(self.ws_name_linedt_1.text())
except WorkspaceException as e:
logger.exception(e)
self.button_feedback_response(str(e),
self.create_workspace_button,
"maroon")
self.refresh_chroot()
def button_feedback_response(self, message, button, colour_str, timeout=2):
"""Changes button colour and displays feedback message for a limited time period.
Args:
message (str): Message to display in button.
button (PyQt5.QWidgets.QBushButton): The button to manipulate.
colour_str (str): The standard CSS colour string or hex code describing the colour to change the button to.
"""
timeout *= 1000
msg_old = button.text()
col_old = button.palette().button().color
txt_col_old = button.palette().buttonText().color
button.setText(message)
button.setStyleSheet(f"background-color: {colour_str}; color: white")
timer = QTimer()
timer.singleShot(
timeout,
lambda: self.reset_button(button, msg_old, col_old, txt_col_old))
@pyqtSlot()
def reset_button(self, button, msg_old, col_old, txt_col_old):
"""Sets a button back to its original display settings.
Args:
button (PyQt5.QWidgets.QBushButton): The button to manipulate.
msg_old (str): Message to display in button.
col_old (str): The standard CSS colour string or hex code describing the colour to change the button to.
txt_col_old (str): The standard CSS colour string or hex code describing the colour to change the button text to.
"""
button.setStyleSheet(f"background-color: {col_old().name()}")
button.setStyleSheet(f"color: {txt_col_old().name()}")
button.setText(msg_old)
button.update()
@pyqtSlot()
def output_config_clicked(self):
"""Outputs pipeline config YAML file on button click."""
out_fname = "pipeline_cfg.yml"
logger.debug(f"Outputting pipeline config: {out_fname}")
with open(out_fname, "w") as outfile:
yaml.dump(self.pipeline_config,
outfile,
default_flow_style=False,
sort_keys=False)
def get_ssh_params(self):
ssh_host = self.ssh_host_linedt.text()
ssh_user = self.ssh_username_linedt.text()
ssh_port = int(self.ssh_port_linedt.text())
return ssh_host, ssh_user, ssh_port
def start_server_over_ssh(self):
params = self.get_ssh_params()
if not all(params):
logger.error(
"Not all SSH parameters given! Not connecting to SSH.")
pass
ssh_host, ssh_user, ssh_port = params
# Pop up dialog to ask for password
text, ok = QInputDialog.getText(None, "Login",
f"Password for {ssh_user}@{ssh_host}",
QLineEdit.Password)
if ok and text:
self.ssh_worker = SSHWorker(params, text, self.run_config)
self.ssh_thread = QThread(self)
self.ssh_worker.moveToThread(self.ssh_thread)
self.ssh_worker.button_message_signal.connect(
self.send_msg_to_run_button)
self.ssh_worker.error_signal.connect(self.on_ssh_error)
self.ssh_worker.finished.connect(self.start_client)
self.ssh_worker.update_ip_linedt_signal.connect(
self.update_ip_linedt)
self.ssh_thread.started.connect(
self.ssh_worker.start_server_over_ssh)
self.ssh_thread.start()
def closeEvent(self, event):
reply = QMessageBox.question(
self,
"Quit",
"Are you sure you want to quit? "
"The server will be stopped.",
QMessageBox.Yes | QMessageBox.No,
QMessageBox.No,
)
if reply == QMessageBox.Yes:
event.accept()
else:
event.ignore()
@pyqtSlot()
def on_ssh_error(self):
self.ssh_error = True
@pyqtSlot(str)
def update_ip_linedt(self, ip):
self.server_ip_linedt.setText(ip)
@pyqtSlot(list)
def send_msg_to_run_button(self, param_list):
self.button_feedback_response(param_list[0], self.run_button,
param_list[1], param_list[2])
@pyqtSlot()
def stop_clicked(self):
logger.debug("Stopping server")
if self.server_process is not None:
self.server_process.kill()
@pyqtSlot()
def run_clicked(self):
"""Starts SuRVoS2 server and client as subprocesses when 'Run' button pressed.
Raises:
Exception: If survos.py not found.
"""
with progress(total=3) as pbar:
pbar.set_description("Starting server...")
pbar.update(1)
self.ssh_error = (
False # Flag which will be set to True if there is an SSH error
)
command_dir = os.path.abspath(os.path.dirname(__file__)) # os.getcwd()
# Set current dir to survos root
from pathlib import Path
command_dir = Path(
command_dir).absolute().parent.parent.parent.resolve()
os.chdir(command_dir)
self.script_fullname = os.path.join(command_dir, "survos.py")
if not os.path.isfile(self.script_fullname):
raise Exception("{}: Script not found".format(
self.script_fullname))
# Retrieve the parameters from the fields TODO: Put some error checking in
self.run_config["workspace_name"] = self.ws_name_linedt_2.text()
self.run_config["server_port"] = self.server_port_linedt.text()
# Temporary measure to check whether the workspace exists or not
full_ws_path = os.path.join(Config["model.chroot"],
self.run_config["workspace_name"])
if not os.path.isdir(full_ws_path):
logger.error(
f"No workspace can be found at {full_ws_path}, Not starting SuRVoS."
)
self.button_feedback_response(
f"Workspace {self.run_config['workspace_name']} does not appear to exist!",
self.run_button,
"maroon",
)
return
pbar.update(1)
# Try some fancy SSH stuff here
if self.ssh_button.isChecked():
self.start_server_over_ssh()
else:
self.server_process = subprocess.Popen([
"python",
self.script_fullname,
"start_server",
self.run_config["workspace_name"],
self.run_config["server_port"],
DataModel.g.CHROOT,
])
try:
outs, errs = self.server_process.communicate(timeout=10)
print(f"OUTS: {outs, errs}")
except subprocess.TimeoutExpired:
pass
# self.start_client()
logger.info(f"setting remote: {self.server_port_linedt.text()}")
remote_ip_port = "127.0.0.1:" + self.server_port_linedt.text()
logger.info(f"setting remote: {remote_ip_port}")
resp = Launcher.g.set_remote(remote_ip_port)
logger.info(f"Response from server to setting remote: {resp}")
cfg.ppw.clientEvent.emit({
"source": "server_tab",
"data": "set_workspace",
"workspace": self.ws_name_linedt_2.text(),
})
cfg.ppw.clientEvent.emit({
"source": "panel_gui",
"data": "refresh",
"value": None
})
#cfg.ppw.clientEvent.emit({'data' : 'view_feature', 'feature_id' : '001_raw'})
pbar.update(1)
@pyqtSlot()
def existing_clicked(self):
ssh_ip = self.server_ip_linedt.text()
remote_ip_port = ssh_ip + ":" + self.server_port_linedt.text()
logger.info(f"setting remote: {remote_ip_port}")
resp = Launcher.g.set_remote(remote_ip_port)
logger.info(f"Response from server to setting remote: {resp}")
cfg.ppw.clientEvent.emit({
"source": "server_tab",
"data": "set_workspace",
"workspace": self.ws_name_linedt_2.text(),
})
cfg.ppw.clientEvent.emit({
"source": "panel_gui",
"data": "refresh",
"value": None
})
def start_client(self):
if not self.ssh_error:
self.button_feedback_response("Starting Client.", self.run_button,
"green", 7)
self.run_config["server_ip"] = self.server_ip_linedt.text()
self.client_process = subprocess.Popen([
"python",
self.script_fullname,
"nu_gui",
self.run_config["workspace_name"],
str(self.run_config["server_ip"]) + ":" +
str(self.run_config["server_port"]),
])
class FrontEndRunner(QWidget):
"""Main FrontEnd Runner window for creating workspace and starting SuRVoS2."""
def __init__(self, run_config, workspace_config, pipeline_config, *args, **kwargs):
super().__init__()
self.run_config = run_config
self.workspace_config = workspace_config
self.pipeline_config = pipeline_config
self.server_process = None
self.client_process = None
pipeline_config_ptree = self.init_ptree(self.pipeline_config, name="Pipeline")
self.layout = QVBoxLayout()
tabwidget = QTabWidget()
tab1 = QWidget()
tab2 = QWidget()
tabwidget.addTab(tab1, "Setup and Start Survos")
tabwidget.addTab(tab2, "Pipeline")
self.create_workspace_button = QPushButton("Create workspace")
tab1.layout = QVBoxLayout()
tab1.setLayout(tab1.layout)
chroot_fields = self.get_chroot_fields()
tab1.layout.addWidget(chroot_fields)
self.setup_adv_run_fields()
self.adv_run_fields.hide()
run_fields = self.get_run_fields()
tab1.layout.addWidget(run_fields)
output_config_button = QPushButton("Save config")
tab2.layout = QVBoxLayout()
tab2.setLayout(tab2.layout)
tab2.layout.addWidget(pipeline_config_ptree)
tab2.layout.addWidget(output_config_button)
self.create_workspace_button.clicked.connect(self.create_workspace_clicked)
output_config_button.clicked.connect(self.output_config_clicked)
self.layout.addWidget(tabwidget)
self.setGeometry(300, 300, 600, 400)
self.setWindowTitle("SuRVoS Settings Editor")
current_fpth = os.path.dirname(os.path.abspath(__file__))
self.setWindowIcon(QIcon(os.path.join(current_fpth, "resources", "logo.png")))
self.setLayout(self.layout)
self.show()
def get_workspace_fields(self):
"""Gets the QGroupBox that contains all the fields for setting up the workspace.
Returns:
PyQt5.QWidgets.GroupBox: GroupBox with workspace fields.
"""
select_data_button = QPushButton("Select")
workspace_fields = QGroupBox("Create Workspace:")
wf_layout = QGridLayout()
wf_layout.addWidget(QLabel("Data File Path:"), 0, 0)
current_data_path = Path(
self.workspace_config["datasets_dir"], self.workspace_config["vol_fname"]
)
self.data_filepth_linedt = QLineEdit(str(current_data_path))
wf_layout.addWidget(self.data_filepth_linedt, 1, 0, 1, 2)
wf_layout.addWidget(select_data_button, 1, 2)
wf_layout.addWidget(QLabel("HDF5 Internal Data Path:"), 2, 0, 1, 1)
ws_dataset_name = self.workspace_config["dataset_name"]
internal_h5_path = (
ws_dataset_name
if str(ws_dataset_name).startswith("/")
else "/" + ws_dataset_name
)
self.h5_intpth_linedt = QLineEdit(internal_h5_path)
wf_layout.addWidget(self.h5_intpth_linedt, 2, 1, 1, 1)
wf_layout.addWidget(QLabel("Workspace Name:"), 3, 0)
self.ws_name_linedt_1 = QLineEdit(self.workspace_config["workspace_name"])
wf_layout.addWidget(self.ws_name_linedt_1, 3, 1)
wf_layout.addWidget(QLabel("Downsample Factor:"), 4, 0)
self.downsample_spinner = QSpinBox()
self.downsample_spinner.setRange(1, 10)
self.downsample_spinner.setSpecialValueText("None")
self.downsample_spinner.setMaximumWidth(60)
self.downsample_spinner.setValue(int(self.workspace_config["downsample_by"]))
wf_layout.addWidget(self.downsample_spinner, 4, 1, 1, 1)
# ROI
self.setup_roi_fields()
wf_layout.addWidget(self.roi_fields, 4, 2, 1, 2)
self.roi_fields.hide()
wf_layout.addWidget(self.create_workspace_button, 5, 0, 1, 3)
workspace_fields.setLayout(wf_layout)
select_data_button.clicked.connect(self.launch_data_loader)
return workspace_fields
def setup_roi_fields(self):
"""Sets up the QGroupBox that displays the ROI dimensions, if selected."""
self.roi_fields = QGroupBox("ROI:")
roi_fields_layout = QHBoxLayout()
# z
roi_fields_layout.addWidget(QLabel("z:"), 0)
self.zstart_roi_val = QLabel("0")
roi_fields_layout.addWidget(self.zstart_roi_val, 1)
roi_fields_layout.addWidget(QLabel("-"), 2)
self.zend_roi_val = QLabel("0")
roi_fields_layout.addWidget(self.zend_roi_val, 3)
# y
roi_fields_layout.addWidget(QLabel("y:"), 4)
self.ystart_roi_val = QLabel("0")
roi_fields_layout.addWidget(self.ystart_roi_val, 5)
roi_fields_layout.addWidget(QLabel("-"), 6)
self.yend_roi_val = QLabel("0")
roi_fields_layout.addWidget(self.yend_roi_val, 7)
# x
roi_fields_layout.addWidget(QLabel("x:"), 8)
self.xstart_roi_val = QLabel("0")
roi_fields_layout.addWidget(self.xstart_roi_val, 9)
roi_fields_layout.addWidget(QLabel("-"), 10)
self.xend_roi_val = QLabel("0")
roi_fields_layout.addWidget(self.xend_roi_val, 11)
self.roi_fields.setLayout(roi_fields_layout)
def setup_adv_run_fields(self):
"""Sets up the QGroupBox that displays the advanced optiona for starting SuRVoS2."""
self.adv_run_fields = QGroupBox("Advanced Run Settings:")
adv_run_layout = QGridLayout()
adv_run_layout.addWidget(QLabel("Server IP Address:"), 0, 0)
self.server_ip_linedt = QLineEdit(self.run_config["server_ip"])
adv_run_layout.addWidget(self.server_ip_linedt, 0, 1)
adv_run_layout.addWidget(QLabel("Server Port:"), 1, 0)
self.server_port_linedt = QLineEdit(self.run_config["server_port"])
adv_run_layout.addWidget(self.server_port_linedt, 1, 1)
# SSH Info
self.ssh_button = QRadioButton("Use SSH")
self.ssh_button.setAutoExclusive(False)
adv_run_layout.addWidget(self.ssh_button, 0, 2)
ssh_flag = self.run_config.get("use_ssh", False)
if ssh_flag:
self.ssh_button.setChecked(True)
self.ssh_button.toggled.connect(self.toggle_ssh)
self.adv_ssh_fields = QGroupBox("SSH Settings:")
adv_ssh_layout = QGridLayout()
adv_ssh_layout.setColumnStretch(2, 2)
ssh_host_label = QLabel("Host")
self.ssh_host_linedt = QLineEdit(self.run_config.get("ssh_host", ""))
adv_ssh_layout.addWidget(ssh_host_label, 0, 0)
adv_ssh_layout.addWidget(self.ssh_host_linedt, 0, 1, 1, 2)
ssh_user_label = QLabel("Username")
self.ssh_username_linedt = QLineEdit(self.get_login_username())
adv_ssh_layout.addWidget(ssh_user_label, 1, 0)
adv_ssh_layout.addWidget(self.ssh_username_linedt, 1, 1, 1, 2)
ssh_port_label = QLabel("Port")
self.ssh_port_linedt = QLineEdit(self.run_config.get("ssh_port", ""))
adv_ssh_layout.addWidget(ssh_port_label, 2, 0)
adv_ssh_layout.addWidget(self.ssh_port_linedt, 2, 1, 1, 2)
self.adv_ssh_fields.setLayout(adv_ssh_layout)
adv_run_layout.addWidget(self.adv_ssh_fields, 1, 2, 2, 5)
self.adv_run_fields.setLayout(adv_run_layout)
def get_run_fields(self):
"""Gets the QGroupBox that contains the fields for starting SuRVoS.
Returns:
PyQt5.QWidgets.GroupBox: GroupBox with run fields.
"""
self.run_button = QPushButton("Run SuRVoS")
advanced_button = QRadioButton("Advanced")
run_fields = QGroupBox("Run SuRVoS:")
run_layout = QGridLayout()
run_layout.addWidget(QLabel("Workspace Name:"), 0, 0)
workspaces = os.listdir(CHROOT)
self.workspaces_list = ComboBox()
for s in workspaces:
self.workspaces_list.addItem(key=s)
run_layout.addWidget(self.workspaces_list, 0, 0)
self.ws_name_linedt_2 = QLineEdit(self.workspace_config["workspace_name"])
self.ws_name_linedt_2.setAlignment(Qt.AlignLeft)
run_layout.addWidget(self.ws_name_linedt_2, 0, 2)
run_layout.addWidget(advanced_button, 1, 0)
run_layout.addWidget(self.adv_run_fields, 2, 1)
run_layout.addWidget(self.run_button, 3, 0, 1, 3)
run_fields.setLayout(run_layout)
advanced_button.toggled.connect(self.toggle_advanced)
self.run_button.clicked.connect(self.run_clicked)
return run_fields
def get_login_username(self):
try:
user = getpass.getuser()
except Exception:
user = ""
return user
@pyqtSlot()
def launch_data_loader(self):
"""Load the dialog box widget to select data with data preview window and ROI selection."""
path = None
int_h5_pth = None
dialog = LoadDataDialog(self)
result = dialog.exec_()
self.roi_limits = None
if result == QDialog.Accepted:
path = dialog.winput.path.text()
int_h5_pth = dialog.int_h5_pth.text()
down_factor = dialog.downsample_spinner.value()
if path and int_h5_pth:
self.data_filepth_linedt.setText(path)
self.h5_intpth_linedt.setText(int_h5_pth)
self.downsample_spinner.setValue(down_factor)
if dialog.roi_changed:
self.roi_limits = tuple(map(str, dialog.get_roi_limits()))
self.roi_fields.show()
self.update_roi_fields_from_dialog()
else:
self.roi_fields.hide()
def update_roi_fields_from_dialog(self):
"""Updates the ROI fields in the main window."""
x_start, x_end, y_start, y_end, z_start, z_end = self.roi_limits
self.xstart_roi_val.setText(x_start)
self.xend_roi_val.setText(x_end)
self.ystart_roi_val.setText(y_start)
self.yend_roi_val.setText(y_end)
self.zstart_roi_val.setText(z_start)
self.zend_roi_val.setText(z_end)
@pyqtSlot()
def toggle_advanced(self):
"""Controls displaying/hiding the advanced run fields on radio button toggle."""
rbutton = self.sender()
if rbutton.isChecked():
self.adv_run_fields.show()
else:
self.adv_run_fields.hide()
@pyqtSlot()
def toggle_ssh(self):
"""Controls displaying/hiding the SSH fields on radio button toggle."""
rbutton = self.sender()
if rbutton.isChecked():
self.adv_ssh_fields.show()
else:
self.adv_ssh_fields.hide()
def setup_ptree_params(self, p, config_dict):
def parameter_tree_change(param, changes):
for param, change, data in changes:
path = p.childPath(param)
if path is not None:
childName = ".".join(path)
else:
childName = param.name()
sibs = param.parent().children()
config_dict[path[-1]] = data
p.sigTreeStateChanged.connect(parameter_tree_change)
def valueChanging(param, value):
pass
for child in p.children():
child.sigValueChanging.connect(valueChanging)
for ch2 in child.children():
ch2.sigValueChanging.connect(valueChanging)
return p
def dict_to_params(self, param_dict, name="Group"):
ptree_param_dicts = []
ctr = 0
for key in param_dict.keys():
entry = param_dict[key]
if type(entry) == str:
d = {"name": key, "type": "str", "value": entry}
elif type(entry) == int:
d = {"name": key, "type": "int", "value": entry}
elif type(entry) == list:
d = {"name": key, "type": "list", "values": entry}
elif type(entry) == float:
d = {"name": key, "type": "float", "value": entry}
elif type(entry) == bool:
d = {"name": key, "type": "bool", "value": entry}
elif type(entry) == dict:
d = self.dict_to_params(entry, name="Subgroup")[0]
d["name"] = key + "_" + str(ctr)
ctr += 1
else:
print(f"Can't handle type {type(entry)}")
ptree_param_dicts.append(d)
ptree_init = [{"name": name, "type": "group", "children": ptree_param_dicts}]
return ptree_init
def init_ptree(self, config_dict, name="Group"):
ptree_init = self.dict_to_params(config_dict, name)
parameters = Parameter.create(
name="ptree_init", type="group", children=ptree_init
)
params = self.setup_ptree_params(parameters, config_dict)
ptree = ParameterTree()
ptree.setParameters(params, showTop=False)
return ptree
@pyqtSlot()
def create_workspace_clicked(self):
"""Performs checks and coordinates workspace creation on button press."""
logger.debug("Creating workspace: ")
# Set the path to the data file
vol_path = Path(self.data_filepth_linedt.text())
if not vol_path.is_file():
err_str = f"No data file exists at {vol_path}!"
logger.error(err_str)
self.button_feedback_response(
err_str, self.create_workspace_button, "maroon"
)
else:
self.workspace_config["datasets_dir"] = str(vol_path.parent)
self.workspace_config["vol_fname"] = str(vol_path.name)
dataset_name = self.h5_intpth_linedt.text()
self.workspace_config["dataset_name"] = str(dataset_name).strip("/")
# Set the workspace name
ws_name = self.ws_name_linedt_1.text()
self.workspace_config["workspace_name"] = ws_name
# Set the downsample factor
ds_factor = self.downsample_spinner.value()
self.workspace_config["downsample_by"] = ds_factor
# Set the ROI limits if they exist
if self.roi_limits:
self.workspace_config["roi_limits"] = self.roi_limits
try:
response = init_ws(self.workspace_config)
_, error = response
if not error:
self.button_feedback_response(
"Workspace created sucessfully",
self.create_workspace_button,
"green",
)
# Update the workspace name in the 'Run' section
self.ws_name_linedt_2.setText(self.ws_name_linedt_1.text())
except WorkspaceException as e:
logger.exception(e)
self.button_feedback_response(
str(e), self.create_workspace_button, "maroon"
)
def button_feedback_response(self, message, button, colour_str, timeout=2):
"""Changes button colour and displays feedback message for a limited time period.
Args:
message (str): Message to display in button.
button (PyQt5.QWidgets.QBushButton): The button to manipulate.
colour_str (str): The standard CSS colour string or hex code describing the colour to change the button to.
"""
timeout *= 1000
msg_old = button.text()
col_old = button.palette().button().color
txt_col_old = button.palette().buttonText().color
button.setText(message)
button.setStyleSheet(f"background-color: {colour_str}; color: white")
timer = QTimer()
timer.singleShot(
timeout, lambda: self.reset_button(button, msg_old, col_old, txt_col_old)
)
@pyqtSlot()
def reset_button(self, button, msg_old, col_old, txt_col_old):
"""Sets a button back to its original display settings.
Args:
button (PyQt5.QWidgets.QBushButton): The button to manipulate.
msg_old (str): Message to display in button.
col_old (str): The standard CSS colour string or hex code describing the colour to change the button to.
txt_col_old (str): The standard CSS colour string or hex code describing the colour to change the button text to.
"""
button.setStyleSheet(f"background-color: {col_old().name()}")
button.setStyleSheet(f"color: {txt_col_old().name()}")
button.setText(msg_old)
button.update()
@pyqtSlot()
def output_config_clicked(self):
"""Outputs pipeline config YAML file on button click."""
out_fname = "pipeline_cfg.yml"
logger.debug(f"Outputting pipeline config: {out_fname}")
with open(out_fname, "w") as outfile:
yaml.dump(
self.pipeline_config, outfile, default_flow_style=False, sort_keys=False
)
def get_ssh_params(self):
ssh_host = self.ssh_host_linedt.text()
ssh_user = self.ssh_username_linedt.text()
ssh_port = int(self.ssh_port_linedt.text())
return ssh_host, ssh_user, ssh_port
def start_server_over_ssh(self):
params = self.get_ssh_params()
if not all(params):
logger.error("Not all SSH parameters given! Not connecting to SSH.")
ssh_host, ssh_user, ssh_port = params
# Pop up dialog to ask for password
text, ok = QInputDialog.getText(
None, "Login", f"Password for {ssh_user}@{ssh_host}", QLineEdit.Password
)
if ok and text:
self.ssh_worker = SSHWorker(params, text, self.run_config)
self.ssh_thread = QThread(self)
self.ssh_worker.moveToThread(self.ssh_thread)
self.ssh_worker.button_message_signal.connect(self.send_msg_to_run_button)
self.ssh_worker.error_signal.connect(self.on_ssh_error)
self.ssh_worker.finished.connect(self.start_client)
self.ssh_worker.update_ip_linedt_signal.connect(self.update_ip_linedt)
self.ssh_thread.started.connect(self.ssh_worker.start_server_over_ssh)
self.ssh_thread.start()
def closeEvent(self, event):
reply = QMessageBox.question(
self,
"Quit",
"Are you sure you want to quit? " "The server will be stopped.",
QMessageBox.Yes | QMessageBox.No,
QMessageBox.No,
)
if reply == QMessageBox.Yes:
event.accept()
else:
event.ignore()
@pyqtSlot()
def on_ssh_error(self):
self.ssh_error = True
@pyqtSlot(str)
def update_ip_linedt(self, ip):
self.server_ip_linedt.setText(ip)
@pyqtSlot(list)
def send_msg_to_run_button(self, param_list):
self.button_feedback_response(
param_list[0], self.run_button, param_list[1], param_list[2]
)
@pyqtSlot()
def run_clicked(self):
"""Starts SuRVoS2 server and client as subprocesses when 'Run' button pressed.
Raises:
Exception: If survos.py not found.
"""
self.ssh_error = (
False # Flag which will be set to True if there is an SSH error
)
command_dir = os.getcwd()
self.script_fullname = os.path.join(command_dir, "survos.py")
if not os.path.isfile(self.script_fullname):
raise Exception("{}: Script not found".format(self.script_fullname))
# Retrieve the parameters from the fields TODO: Put some error checking in
self.run_config["workspace_name"] = self.ws_name_linedt_2.text()
self.run_config["server_port"] = self.server_port_linedt.text()
# Temporary measure to check whether the workspace exists or not
full_ws_path = os.path.join(
Config["model.chroot"], self.run_config["workspace_name"]
)
if not os.path.isdir(full_ws_path):
logger.error(
f"No workspace can be found at {full_ws_path}, Not starting SuRVoS."
)
self.button_feedback_response(
f"Workspace {self.run_config['workspace_name']} does not appear to exist!",
self.run_button,
"maroon",
)
return
# Try some fancy SSH stuff here
if self.ssh_button.isChecked():
self.start_server_over_ssh()
else:
self.server_process = subprocess.Popen(
[
"python",
self.script_fullname,
"start_server",
self.run_config["workspace_name"],
self.run_config["server_port"],
]
)
try:
outs, errs = self.server_process.communicate(timeout=10)
print(f"OUTS: {outs, errs}")
except subprocess.TimeoutExpired:
pass
self.start_client()
def start_client(self):
if not self.ssh_error:
self.button_feedback_response(
"Starting Client.", self.run_button, "green", 7
)
self.run_config["server_ip"] = self.server_ip_linedt.text()
self.client_process = subprocess.Popen(
[
"python",
self.script_fullname,
"nu_gui",
self.run_config["workspace_name"],
str(self.run_config["server_ip"])
+ ":"
+ str(self.run_config["server_port"]),
]
)