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fixes to build version 1.1.3

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This commit is contained in:
Tyler
2025-10-15 12:59:24 -07:00
parent d6c71e0ab2
commit 3e0f70ea49
5 changed files with 82 additions and 72 deletions
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137
main.py
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@@ -42,6 +42,7 @@ from PySide6.QtWidgets import (
)
from PySide6.QtCore import QThread, Signal, Qt, QTimer, QEvent, QSize
from PySide6.QtGui import QAction, QKeySequence, QIcon, QIntValidator, QDoubleValidator, QPixmap, QStandardItemModel, QStandardItem
from PySide6.QtSvgWidgets import QSvgWidget # needed to show svgs when app is not frozen
CURRENT_VERSION = "1.0.1"
@@ -173,10 +174,10 @@ SECTIONS = [
class CommandConsole(QWidget):
class TerminalWindow(QWidget):
def __init__(self, parent=None):
super().__init__(parent, Qt.WindowType.Window)
self.setWindowTitle("Custom Console")
self.setWindowTitle("Terminal - FLARES")
self.output_area = QTextEdit()
self.output_area.setReadOnly(True)
@@ -189,10 +190,8 @@ class CommandConsole(QWidget):
layout.addWidget(self.input_line)
self.setLayout(layout)
# Define your commands
self.commands = {
"hello": self.cmd_hello,
"add": self.cmd_add,
"help": self.cmd_help
}
@@ -219,12 +218,9 @@ class CommandConsole(QWidget):
else:
self.output_area.append(f"[Unknown command] '{command_name}'")
# Example commands
def cmd_hello(self, *args):
return "Hello from the console!"
def cmd_add(self, a, b):
return f"Result: {int(a) + int(b)}"
def cmd_hello(self, *args):
return "Hello from the terminal!"
def cmd_help(self, *args):
return f"Available commands: {', '.join(self.commands.keys())}"
@@ -734,13 +730,12 @@ class UpdateEventsWindow(QWidget):
self.description = QLabel()
self.description.setTextFormat(Qt.TextFormat.RichText)
self.description.setTextInteractionFlags(Qt.TextInteractionFlag.TextBrowserInteraction)
self.description.setOpenExternalLinks(False) # Handle the click internally
self.description.setOpenExternalLinks(True)
self.description.setText("Some software when creating snirf files will insert a template of optode positions as the correct position of the optodes for the participant.<br>"
"This is rarely correct as each head differs slightly in shape or size, and a lot of calculations require the optodes to be in the correct location.<br>"
"Using a .txt file, we can update the positions in the snirf file to match those of a digitization system such as one from Polhemus or elsewhere.<br>"
"The .txt file should have the fiducials, detectors, and sources clearly labeled, followed by the x, y, and z coordinates seperated by a space.<br>"
"An example format of what a digitization text file should look like can be found <a href='custom_link'>by clicking here</a>.")
self.description.setText("The events that are present in a snirf file may not be the events that are to be studied and examined.<br>"
"Utilizing different software and video recordings, it is easy enough to see when an action actually occured in a file.<br>"
"The software <a href='https://www.boris.unito.it/'>BORIS</a> is used to add these events to video files, and these events can be applied to the snirf file <br>"
"selected below by selecting the correct BORIS observation and time syncing it to an event that it shares with the snirf file.")
layout.addWidget(self.description)
@@ -2196,12 +2191,13 @@ class ParticipantFoldChannelsWidget(QWidget):
self.image_index_dropdown.currentIndexChanged.connect(self.update_image_index_dropdown_label)
self.submit_button = QPushButton("Submit")
self.submit_button.clicked.connect(self.show_brain_images)
self.submit_button.clicked.connect(self.show_fold_images)
self.top_bar.addWidget(QLabel("Participants:"))
self.top_bar.addWidget(self.participant_dropdown)
self.top_bar.addWidget(QLabel("Fold Type:"))
self.top_bar.addWidget(self.image_index_dropdown)
self.top_bar.addWidget(QLabel("This will cause the app to hang for ~30s!"))
self.top_bar.addWidget(self.submit_button)
self.scroll = QScrollArea()
@@ -2321,7 +2317,7 @@ class ParticipantFoldChannelsWidget(QWidget):
index_labels = [s.split(" ")[0] for s in selected]
self.image_index_dropdown.lineEdit().setText(", ".join(index_labels))
def show_brain_images(self):
def show_fold_images(self):
import flares
selected_display_names = self._get_checked_items(self.participant_dropdown)
@@ -2337,42 +2333,6 @@ class ParticipantFoldChannelsWidget(QWidget):
int(s.split(" ")[0]) for s in self._get_checked_items(self.image_index_dropdown)
]
parameterized_indexes = {
0: [
{
"key": "show_optodes",
"label": "Determine what is rendered above the brain. Valid values are 'sensors', 'labels', 'none', 'all'.",
"default": "all",
"type": str,
},
{
"key": "show_brodmann",
"label": "Show common brodmann areas on the brain.",
"default": "True",
"type": bool,
}
],
}
# Inject full_text from index_texts
for idx, params_list in parameterized_indexes.items():
full_text = self.index_texts[idx] if idx < len(self.index_texts) else f"{idx} (No label found)"
for param_info in params_list:
param_info["full_text"] = full_text
indexes_needing_params = {idx: parameterized_indexes[idx] for idx in selected_indexes if idx in parameterized_indexes}
param_values = {}
if indexes_needing_params:
dialog = ParameterInputDialog(indexes_needing_params, parent=self)
if dialog.exec_() == QDialog.Accepted:
param_values = dialog.get_values()
if param_values is None:
return
else:
return
# Pass the necessary arguments to each method
for file_path in selected_file_paths:
haemo_obj = self.haemo_dict.get(file_path)
@@ -2385,14 +2345,6 @@ class ParticipantFoldChannelsWidget(QWidget):
for idx in selected_indexes:
if idx == 0:
params = param_values.get(idx, {})
show_optodes = params.get("show_optodes", None)
show_brodmann = params.get("show_brodmann", None)
if show_optodes is None or show_brodmann is None:
print(f"Missing parameters for index {idx}, skipping.")
continue
flares.fold_channels(haemo_obj)
else:
@@ -2605,7 +2557,7 @@ class GroupViewerWidget(QWidget):
self.index_texts = [
"0 (GLM Results)",
"1 (Significance)",
# "2 (third_image)",
"2 (Brain Activity Visualization)",
# "3 (fourth image)",
]
@@ -2908,6 +2860,32 @@ class GroupViewerWidget(QWidget):
"type": float,
}
],
2: [
{
"key": "show_optodes",
"label": "Determine what is rendered above the brain. Valid values are 'sensors', 'labels', 'none', 'all'.",
"default": "all",
"type": str,
},
{
"key": "t_or_theta",
"label": "Specify if t values or theta values should be plotted. Valid values are 't', 'theta'",
"default": "theta",
"type": str,
},
{
"key": "show_text",
"label": "Display informative text on the top left corner. THIS DOES NOT WORK AND SHOULD BE LEFT AT FALSE",
"default": "False",
"type": bool,
},
{
"key": "brain_bounds",
"label": "Graph Upper/Lower Limit",
"default": "1.0",
"type": float,
}
],
}
# Inject full_text from index_texts
@@ -2930,8 +2908,13 @@ class GroupViewerWidget(QWidget):
all_cha = pd.DataFrame()
for fp in selected_file_paths:
cha_df = self.cha.get(fp)
for file_path in selected_file_paths:
haemo_obj = self.haemo_dict.get(file_path)
if haemo_obj is None:
continue
cha_df = self.cha.get(file_path)
if cha_df is not None:
all_cha = pd.concat([all_cha, cha_df], ignore_index=True)
@@ -2986,6 +2969,20 @@ class GroupViewerWidget(QWidget):
df_contrasts = pd.concat(all_contrasts, ignore_index=True)
flares.run_second_level_analysis(df_contrasts, p_haemo, p_val, graph_bounds)
elif idx == 2:
params = param_values.get(idx, {})
show_optodes = params.get("show_optodes", None)
t_or_theta = params.get("t_or_theta", None)
show_text = params.get("show_text", None)
brain_bounds = params.get("brain_bounds", None)
if show_optodes is None or t_or_theta is None or show_text is None or brain_bounds is None:
print(f"Missing parameters for index {idx}, skipping.")
continue
flares.brain_3d_visualization(haemo_obj, all_cha, selected_event, t_or_theta=t_or_theta, show_optodes=show_optodes, show_text=show_text, brain_bounds=brain_bounds)
elif idx == 3:
pass
@@ -3840,8 +3837,8 @@ class MainApplication(QMainWindow):
options_actions = [
("User Guide", "F1", self.user_guide, resource_path("icons/help_24dp_1F1F1F.svg")),
("Check for Updates", "F5", self.manual_check_for_updates, resource_path("icons/update_24dp_1F1F1F.svg")),
("Update optodes in snirf file...", "F6", self.update_optode_positions, resource_path("icons/update_24dp_1F1F1F.svg")),
("Update events in snirf file...", "F7", self.update_event_markers, resource_path("icons/update_24dp_1F1F1F.svg")),
("Update optodes in snirf file...", "F6", self.update_optode_positions, resource_path("icons/upgrade_24dp_1F1F1F.svg")),
("Update events in snirf file...", "F7", self.update_event_markers, resource_path("icons/upgrade_24dp_1F1F1F.svg")),
("About", "F12", self.about_window, resource_path("icons/info_24dp_1F1F1F.svg"))
]
@@ -3852,9 +3849,7 @@ class MainApplication(QMainWindow):
terminal_menu = menu_bar.addMenu("Terminal")
terminal_actions = [
("Cut", "Ctrl+X", self.terminal_gui, resource_path("icons/content_cut_24dp_1F1F1F.svg")),
("Copy", "Ctrl+C", self.terminal_gui, resource_path("icons/content_copy_24dp_1F1F1F.svg")),
("Paste", "Ctrl+V", self.terminal_gui, resource_path("icons/content_paste_24dp_1F1F1F.svg"))
("New Terminal", "Ctrl+Alt+T", self.terminal_gui, resource_path("icons/terminal_24dp_1F1F1F.svg")),
]
for name, shortcut, slot, icon in terminal_actions:
terminal_menu.addAction(make_action(name, shortcut, slot, icon=icon))
@@ -3945,7 +3940,7 @@ class MainApplication(QMainWindow):
def terminal_gui(self):
if self.terminal is None or not self.terminal.isVisible():
self.terminal = CommandConsole(self)
self.terminal = TerminalWindow(self)
self.terminal.show()
def update_optode_positions(self):
@@ -4865,7 +4860,7 @@ def resource_path(relative_path):
# PyInstaller bundle path
base_path = sys._MEIPASS
else:
base_path = os.path.abspath(".")
base_path = os.path.dirname(os.path.abspath(__file__))
return os.path.join(base_path, relative_path)