Coverage for main/ui/skull_stripping_page.py: 96%
293 statements
« prev ^ index » next coverage.py v7.15.0, created at 2026-07-03 15:51 +0000
1import torch
2from PyQt6.QtWidgets import (
3 QVBoxLayout, QLabel, QPushButton, QMessageBox, QCheckBox,
4 QHBoxLayout, QWidget, QDoubleSpinBox, QSpinBox, QGroupBox,
5 QProgressBar, QFrame
6)
7from PyQt6.QtCore import Qt, pyqtSignal, QCoreApplication
8import os
9import subprocess
11from components.file_selector_widget import FileSelectorWidget
12from threads.skull_strip_thread import SkullStripThread
13from page import Page
14from logger import get_logger
16log = get_logger()
19class SkullStrippingPage(Page):
20 """
21 GUI page for performing skull stripping on NIfTI files.
23 This class provides a user interface to select anatomical MRI images
24 and perform skull stripping using either:
25 - BET (Brain Extraction Tool) from FSL (if available)
26 - HD-BET (deep learning-based alternative)
28 It handles:
29 * User input for tool parameters
30 * Background processing using a worker thread
31 * Progress and status updates
33 Signals:
34 processing (bool): emitted when processing starts or stops.
35 """
37 processing = pyqtSignal(bool)
39 def __init__(self, context=None, previous_page=None):
40 """
41 Initialize the SkullStrippingPage.
43 Args:
44 context (dict, optional): Shared app context for state and communication.
45 previous_page (Page, optional): Reference to previous navigation page.
46 """
47 super().__init__()
48 self.canceled = False
49 self.context = context
50 self.previous_page = previous_page
51 self.next_page = None
52 self.worker = None # Background thread reference
53 self.has_cuda = torch.cuda.is_available()
54 self.bet_tool = ""
56 self._setup_ui()
57 self._translate_ui()
59 # Re-translate if app language changes
60 if context and "language_changed" in context:
61 context["language_changed"].connect(self._translate_ui)
63 def _setup_ui(self):
64 """Create and configure all UI components."""
65 self.processing.connect(self.set_processing_mode)
66 self.layout = QVBoxLayout(self)
67 self.setLayout(self.layout)
69 # Title
70 self.title = QLabel("Select a NIfTI file for Skull Stripping")
71 self.title.setStyleSheet("font-size: 18px; font-weight: bold;")
72 self.title.setAlignment(Qt.AlignmentFlag.AlignCenter)
73 self.layout.addWidget(self.title)
75 # Info label (link to BET or HD-BET)
76 self.info_label = QLabel(
77 'Using tool: <a href="https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BET">BET from FSL toolkit</a>'
78 )
79 self.info_label.setOpenExternalLinks(True)
80 self.info_label.setTextInteractionFlags(Qt.TextInteractionFlag.TextBrowserInteraction)
81 self.info_label.setStyleSheet("""
82 font-size: 11px;
83 color: #666;
84 font-style: italic;
85 margin-bottom: 6px;
86 """)
87 self.info_label.setAlignment(Qt.AlignmentFlag.AlignCenter)
88 self.info_label.setWordWrap(True)
89 self.layout.addWidget(self.info_label)
91 # File selector widget for NIfTI files
92 self.file_selector_widget = FileSelectorWidget(
93 parent=self,
94 context=self.context,
95 has_existing_function=self.has_existing_skull_strip,
96 label="skull strip",
97 allow_multiple=True,
98 processing=self.processing,
99 forced_filters={"datatype": "anat"}
100 )
101 self.layout.addWidget(self.file_selector_widget)
103 # Check if BET command exists in system
104 try:
105 subprocess.run(['bet'], stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
106 self.has_bet = True
107 except FileNotFoundError:
108 self.has_bet = False
110 # Setup parameters for BET (if installed)
111 if self.has_bet:
112 self._setup_bet_options()
113 else:
114 try:
115 subprocess.run(['mri_synthstrip'], stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
116 self.has_synthstrip = True
117 except FileNotFoundError:
118 self.has_synthstrip = False
120 if self.has_synthstrip:
121 self.info_label.setText(
122 QCoreApplication.translate("SkullStrippingPage", 'Using tool: <a href="https://surfer.nmr.mgh.harvard.edu/docs/synthstrip/">SynthStrip</a> <br>')
123 )
124 else:
125 self.info_label.setText(
126 QCoreApplication.translate("SkullStrippingPage",
127 'Using tool: <a href="https://github.com/MIC-DKFZ/HD-BET">hd-bet</a> <br>'
128 'To use BET from FSL toolkit, install it following the instructions at: '
129 '<a href="https://fsl.fmrib.ox.ac.uk/fsl/docs/#/install/index">FSL installation</a>')
130 )
131 self.info_label.setOpenExternalLinks(True)
132 self.info_label.setTextInteractionFlags(Qt.TextInteractionFlag.TextBrowserInteraction)
133 self.info_label.setToolTip("Open link")
135 # Progress bar
136 self.progress_bar = QProgressBar()
137 self.progress_bar.setVisible(False)
138 self.layout.addWidget(self.progress_bar)
140 # Action buttons (Run / Cancel)
141 button_frame = QFrame()
142 button_layout = QHBoxLayout(button_frame)
143 button_layout.setContentsMargins(0, 15, 0, 0)
145 # --- RUN button (green) ---
146 self.run_button = QPushButton("Run Skull Stripping")
147 self.file_selector_widget.has_file.connect(self.run_button.setEnabled)
148 self.run_button.setEnabled(False)
149 self.run_button.clicked.connect(self.run_bet)
150 self.run_button.setStyleSheet("""
151 QPushButton {
152 font-size: 14px;
153 font-weight: bold;
154 background-color: #27ae60;
155 color: white;
156 border-radius: 8px;
157 padding: 10px 20px;
158 min-width: 140px;
159 }
160 QPushButton:hover {
161 background-color: #229954;
162 }
163 QPushButton:disabled {
164 background-color: #bdc3c7;
165 color: #7f8c8d;
166 }
167 """)
168 button_layout.addStretch()
169 button_layout.addWidget(self.run_button)
171 # --- CANCEL button (red) ---
172 self.cancel_button = QPushButton("Stop Processing")
173 self.cancel_button.setVisible(False)
174 self.cancel_button.clicked.connect(self.cancel_processing)
175 self.cancel_button.setStyleSheet("""
176 QPushButton {
177 font-size: 14px;
178 font-weight: bold;
179 background-color: #e74c3c;
180 color: white;
181 border-radius: 8px;
182 padding: 10px 20px;
183 min-width: 140px;
184 }
185 QPushButton:hover {
186 background-color: #c0392b;
187 }
188 QPushButton:disabled {
189 background-color: #bdc3c7;
190 color: #7f8c8d;
191 }
192 """)
193 button_layout.addWidget(self.cancel_button)
194 button_layout.addStretch()
196 self.layout.addWidget(button_frame)
198 # Stato
199 self.status_label = QLabel("")
200 self.status_label.setAlignment(Qt.AlignmentFlag.AlignCenter)
201 self.layout.addWidget(self.status_label)
203 def _setup_bet_options(self):
204 """Setup BET-specific parameter inputs and advanced options."""
205 # Fractional intensity threshold (main parameter)
206 self.f_box = QGroupBox()
207 f_layout = QHBoxLayout()
208 self.f_label = QLabel("Fractional intensity threshold, smaller values give larger brain outline estimates")
209 f_layout.addWidget(self.f_label)
211 self.f_spinbox = QDoubleSpinBox()
212 self.f_spinbox.setRange(0.0, 1.0)
213 self.f_spinbox.setSingleStep(0.05)
214 self.f_spinbox.setValue(0.50)
215 self.f_spinbox.setDecimals(2)
216 self.f_spinbox.setMinimumWidth(60)
217 self.f_spinbox.setMaximumWidth(80)
218 f_layout.addWidget(self.f_spinbox)
219 f_layout.addStretch()
220 self.f_box.setLayout(f_layout)
221 self.layout.addWidget(self.f_box)
223 # Toggle for advanced options
224 self.advanced_btn = QPushButton("Show Advanced Options")
225 self.advanced_btn.setCheckable(True)
226 self.advanced_btn.clicked.connect(self.toggle_advanced)
227 self.layout.addWidget(self.advanced_btn)
229 # Advanced parameters box
230 self.is_checked = False
231 self.advanced_box = QGroupBox()
232 self.advanced_layout = QVBoxLayout()
234 # Output options
235 self.output_label = QLabel("Advanced options:")
236 self.output_label.setStyleSheet("font-weight: bold; margin-top: 5px;")
237 self.advanced_layout.addWidget(self.output_label)
239 self.opt_brain_extracted = QCheckBox("Output brain-extracted image")
240 self.opt_brain_extracted.setChecked(True)
241 self.advanced_layout.addWidget(self.opt_brain_extracted)
243 self.opt_m = QCheckBox("Output binary brain mask image")
244 self.advanced_layout.addWidget(self.opt_m)
246 self.opt_t = QCheckBox("Apply thresholding to brain and mask image")
247 self.advanced_layout.addWidget(self.opt_t)
249 self.opt_s = QCheckBox("Output exterior skull surface image")
250 self.advanced_layout.addWidget(self.opt_s)
252 self.opt_o = QCheckBox("Output brain surface overlaid onto original image")
253 self.advanced_layout.addWidget(self.opt_o)
255 # Threshold gradient
256 self.threshold_layout = QHBoxLayout()
257 self.threshold_label = QLabel("Threshold gradient; positive values give larger brain outline at bottom, smaller at top")
258 self.threshold_layout.addWidget(self.threshold_label)
259 self.g_spinbox = QDoubleSpinBox()
260 self.g_spinbox.setRange(-1.0, 1.0)
261 self.g_spinbox.setSingleStep(0.1)
262 self.g_spinbox.setValue(0.0)
263 self.g_spinbox.setDecimals(1)
264 self.g_spinbox.setMinimumWidth(60)
265 self.g_spinbox.setMaximumWidth(80)
266 self.threshold_layout.addWidget(self.g_spinbox)
267 self.threshold_layout.addStretch()
268 self.advanced_layout.addLayout(self.threshold_layout)
270 # Sphere coordinates
271 coords_layout = QHBoxLayout()
272 self.coords_label = QLabel("Coordinates (voxels) for centre of initial brain surface sphere")
273 coords_layout.addWidget(self.coords_label)
275 self.c_x_spinbox = QSpinBox()
276 self.c_x_spinbox.setRange(0, 9999)
277 coords_layout.addWidget(self.c_x_spinbox)
278 coords_layout.addWidget(QLabel("Y"))
280 self.c_y_spinbox = QSpinBox()
281 self.c_y_spinbox.setRange(0, 9999)
282 coords_layout.addWidget(self.c_y_spinbox)
283 coords_layout.addWidget(QLabel("Z"))
285 self.c_z_spinbox = QSpinBox()
286 self.c_z_spinbox.setRange(0, 9999)
287 coords_layout.addWidget(self.c_z_spinbox)
288 coords_layout.addStretch()
290 self.advanced_layout.addLayout(coords_layout)
291 self.advanced_box.setLayout(self.advanced_layout)
292 self.advanced_box.setVisible(False)
293 self.layout.addWidget(self.advanced_box)
295 def has_existing_skull_strip(self, nifti_file_path, workspace_path):
296 """
297 Check if a skull-stripped file already exists for the selected subject.
299 Args:
300 nifti_file_path (str): Full path to input NIfTI file.
301 workspace_path (str): Base workspace directory path.
303 Returns:
304 bool: True if an existing skull strip is found, False otherwise.
305 """
306 path_parts = nifti_file_path.replace(workspace_path, '').strip(os.sep).split(os.sep)
307 subject_id = next((p for p in path_parts if p.startswith('sub-')), None)
308 if not subject_id:
309 return False
311 skull_strip_dir = os.path.join(workspace_path, 'derivatives', 'skullstrips', subject_id, 'anat')
312 if not os.path.exists(skull_strip_dir):
313 return False
315 return any(f.endswith('.nii.gz') for f in os.listdir(skull_strip_dir))
317 def toggle_advanced(self):
318 """Toggle visibility of advanced BET parameters."""
319 self.is_checked = self.advanced_btn.isChecked()
320 self.advanced_box.setVisible(self.is_checked)
321 self.advanced_btn.setText("Hide Advanced Options" if self.is_checked else "Show Advanced Options")
323 def run_bet(self):
324 """Start the skull stripping process in a background thread."""
325 selected_files = self.file_selector_widget.get_selected_files()
326 if not selected_files:
327 QMessageBox.warning(self, "No files", "Please select at least one NIfTI file first.")
328 return
330 parameters = None
331 if self.has_bet:
332 parameters = {
333 'f_val': self.f_spinbox.value(),
334 'opt_brain_extracted': self.opt_brain_extracted.isChecked(),
335 'opt_m': self.opt_m.isChecked(),
336 'opt_t': self.opt_t.isChecked(),
337 'opt_s': self.opt_s.isChecked(),
338 'opt_o': self.opt_o.isChecked(),
339 'g_val': self.g_spinbox.value(),
340 'c_x': self.c_x_spinbox.value(),
341 'c_y': self.c_y_spinbox.value(),
342 'c_z': self.c_z_spinbox.value(),
343 }
345 if self.has_bet:
346 self.bet_tool = "fsl-bet"
347 elif self.has_synthstrip:
348 self.bet_tool = "synthstrip"
349 else:
350 self.bet_tool = "hd-bet"
352 # Create worker thread
353 self.worker = SkullStripThread(selected_files, self.context["workspace_path"], parameters, self.has_cuda, self.bet_tool)
355 # Connect worker signals
356 self.worker.progress_updated.connect(self.on_progress_updated)
357 self.worker.progress_value_updated.connect(self.on_progress_value_updated)
358 self.worker.file_started.connect(self.on_file_started)
359 self.worker.file_completed.connect(self.on_file_completed)
360 self.worker.all_completed.connect(self.on_all_completed)
361 self.worker.finished.connect(self.on_worker_finished)
363 # Update UI
364 self.processing.emit(True)
365 self.progress_bar.setRange(0, 100)
366 self.progress_bar.setValue(0)
367 self.progress_bar.setVisible(True)
369 self.worker.start()
371 def cancel_processing(self):
372 """Cancel the currently running process."""
373 self.canceled = True
374 if self.worker and self.worker.isRunning():
376 self.worker.cancel()
377 self.status_label.setText("Cancelling...")
378 self.status_label.setStyleSheet("color: #FF9800; font-weight: bold;")
380 def set_processing_mode(self, processing):
381 """Enable or disable UI controls depending on processing state."""
382 self.run_button.setVisible(not processing and bool(self.file_selector_widget.get_selected_files()))
383 self.cancel_button.setVisible(processing)
384 if hasattr(self, "f_spinbox"):
385 self.f_spinbox.setEnabled(not processing)
386 if hasattr(self, "advanced_btn"):
387 self.advanced_btn.setEnabled(not processing)
388 if hasattr(self, "advanced_box"):
389 for widget in self.advanced_box.findChildren(QWidget):
390 widget.setEnabled(not processing)
391 self.cancel_button.setVisible(processing)
394 def on_progress_updated(self, message):
395 """Update progress text message."""
396 self.status_label.setText(message)
397 self.status_label.setStyleSheet("color: #2196F3; font-weight: bold;")
399 def on_progress_value_updated(self, value):
400 """Update numeric progress bar value."""
401 self.progress_bar.setValue(value)
403 def on_file_started(self, filename):
404 """Triggered when a new file starts processing."""
405 pass
407 def on_file_completed(self, filename, success, error_message):
408 """Triggered when a file finishes processing."""
409 if not success and error_message:
410 log.error(f"Error processing {filename}: {error_message}")
412 def on_all_completed(self, success_count, failed_files):
413 """Triggered after all files are processed."""
414 # Nascondi progress bar
415 self.progress_bar.setVisible(False)
417 # Aggiorna il messaggio di stato finale
418 if success_count > 0:
419 summary = QCoreApplication.translate("SkullStrippingPage",
420 "Skull Stripping completed successfully for {0} file(s)").format(
421 success_count)
422 if failed_files:
423 failed_summary = QCoreApplication.translate("SkullStrippingPage",
424 "{count} file(s) failed: {files}").format(
425 count=len(failed_files),
426 files=', '.join([os.path.basename(f) for f in failed_files])
427 )
428 summary += f"\n{failed_summary}"
429 self.status_label.setStyleSheet("color: #FF9800; font-weight: bold; font-size: 12pt; padding: 5px;")
430 else:
431 self.status_label.setStyleSheet("color: #4CAF50; font-weight: bold; font-size: 12pt; padding: 5px;")
432 else:
433 failed_files_num = len(failed_files)
434 if failed_files_num == 0:
435 failed_files_num = ""
436 summary = QCoreApplication.translate("SkullStrippingPage", "All {0} file(s) failed to process").format(
437 failed_files_num)
438 self.status_label.setStyleSheet("color: #FF0000; font-weight: bold; font-size: 12pt; padding: 5px;")
440 self.status_label.setText(summary)
443 def on_worker_finished(self):
444 """Triggered when worker thread finishes execution."""
445 self.processing.emit(False)
446 if self.worker:
447 self.worker.deleteLater()
448 self.worker = None
449 if self.context and "update_main_buttons" in self.context:
450 self.context["update_main_buttons"]()
452 def back(self):
453 """Navigate back to the previous page if not processing."""
454 if self.worker and self.worker.isRunning():
455 QMessageBox.warning(self, "Processing in progress",
456 "Cannot go back while skull stripping is in progress. Please wait or cancel.")
457 log.warning("Processing in progress")
458 return None
459 if self.previous_page:
460 self.previous_page.on_enter()
461 return self.previous_page
462 return None
464 def on_enter(self):
465 """Reset status label when page is entered."""
466 self.status_label.setText("")
468 def is_ready_to_advance(self):
469 """Return False since this page doesn't advance automatically."""
470 return False
472 def is_ready_to_go_back(self):
473 """Disable back navigation during processing."""
474 return not (self.worker and self.worker.isRunning())
476 def reset_page(self):
477 """Reset the page state to its initial configuration."""
478 if self.worker and self.worker.isRunning():
479 self.worker.cancel()
480 self.worker.wait()
482 self.file_selector_widget.clear_selected_files()
483 self.run_button.setEnabled(False)
485 # Reset advanced options
486 self.f_spinbox.setValue(0.50)
487 self.advanced_btn.setChecked(False)
488 self.advanced_box.setVisible(False)
489 self.advanced_btn.setText("Show Advanced Options")
491 self.opt_brain_extracted.setChecked(True)
492 self.opt_m.setChecked(False)
493 self.opt_t.setChecked(False)
494 self.opt_s.setChecked(False)
495 self.opt_o.setChecked(False)
497 self.g_spinbox.setValue(0.0)
498 self.c_x_spinbox.setValue(0)
499 self.c_y_spinbox.setValue(0)
500 self.c_z_spinbox.setValue(0)
502 self.progress_bar.setVisible(False)
503 self.cancel_button.setVisible(False)
504 self.processing.emit(False)
505 self.status_label.setText("")
507 def _translate_ui(self):
508 """Translate UI strings according to the active language."""
509 self.title.setText(QCoreApplication.translate("SkullStrippingPage", "Select a NIfTI file for Skull Stripping"))
510 if self.has_bet:
511 self.f_label.setText(QCoreApplication.translate("SkullStrippingPage", "Fractional intensity threshold, smaller values give larger brain outline estimates"))
512 self.advanced_btn.setText(QCoreApplication.translate("SkullStrippingPage", "Show Advanced Options"))
513 self.output_label.setText(QCoreApplication.translate("SkullStrippingPage", "Advanced options:"))
514 self.opt_brain_extracted.setText(QCoreApplication.translate("SkullStrippingPage", "Output brain-extracted image"))
515 self.opt_m.setText(QCoreApplication.translate("SkullStrippingPage", "Output binary brain mask image"))
516 self.opt_t.setText(QCoreApplication.translate("SkullStrippingPage", "Apply thresholding to brain and mask image"))
517 self.opt_s.setText(QCoreApplication.translate("SkullStrippingPage", "Output exterior skull surface image"))
518 self.opt_o.setText(QCoreApplication.translate("SkullStrippingPage", "Output brain surface overlaid onto original image"))
519 self.threshold_label.setText(QCoreApplication.translate("SkullStrippingPage", "Threshold gradient; positive values give larger brain outline at bottom, smaller at top"))
520 self.coords_label.setText(QCoreApplication.translate("SkullStrippingPage", "Coordinates (voxels) for centre of initial brain surface sphere"))
521 else:
522 self.info_label.setToolTip(QCoreApplication.translate("SkullStrippingPage", "Open link"))
524 self.run_button.setText(QCoreApplication.translate("SkullStrippingPage", "Run Skull Stripping"))
525 self.cancel_button.setText(QCoreApplication.translate("SkullStrippingPage", "Cancel"))