move import

changelog.md

@@ -0,0 +1,17 @@
+# Version 1.0.1
+
+- Two new options have been added when clicking on a participant's file.
+- First new option is Age which allows the option to specify age on a per-file basis to calculate DPF by using the Scholkmann & Wolf calculation instead of having one DPF for all files. Fixes [Issue 1](https://git.research.dezeeuw.ca/tyler/flares/issues/1). This also allows for proper calculation of DPF for the two seperate wavelengths.
+- If no age is set by the user, the code will fall back to the age of 25
+- Second new option is Gender to be used in future analysis options (currently not implemented).
+- UI elements have been shuffled to make room for the new parameters.
+- Removed the process button from being available until a file or project is opened. Fixes [Issue 2](https://git.research.dezeeuw.ca/tyler/flares/issues/2).
+- Removed the option for PPF under Haemoglobin Concentration as it is no longer used.
+- Added a new category in the options called Other
+- Added MAX_WORKERS to the Other category. This is how many files should be processed at once. Fixes [Issue 13](https://git.research.dezeeuw.ca/tyler/flares/issues/13).
+- Added more information about the snirf file to be displayed when selected
+
+
+# Version 1.0.0
+
+- Initial release.

fNIRS_module.py

@@ -24,6 +24,7 @@ from multiprocessing import Queue
 from typing import Any, Optional, cast, Literal, Iterator, Union
 
 # External library imports
+import h5py
 import pywt # type: ignore
 import qtpy # type: ignore
 import xlrd # type: ignore
@@ -42,14 +43,14 @@ from pandas import DataFrame
 import matplotlib.pyplot as plt
 from matplotlib.axes import Axes
 from numpy.typing import NDArray
-import vtkmodules.util.data_model
+#import vtkmodules.util.data_model
 from numpy import floating, float64
 from matplotlib.lines import Line2D
 import matplotlib.colors as mcolors
 from scipy.stats import ttest_1samp # type: ignore
 from matplotlib.figure import Figure
 import statsmodels.formula.api as smf # type: ignore
-import vtkmodules.util.execution_model
+#import vtkmodules.util.execution_model
 from nilearn.plotting import plot_design_matrix # type: ignore
 from scipy.signal import welch, butter, filtfilt # type: ignore
 from matplotlib.colors import LinearSegmentedColormap
@@ -127,7 +128,7 @@ EXCLUDE_CHANNELS: bool
 MAX_BAD_CHANNELS: int
 LONG_CHANNEL_THRESH: float
 
-PPF: float
+METADATA: dict
 
 DRIFT_MODEL: str
 DURATION_BETWEEN_ACTIVITIES: int
@@ -223,7 +224,7 @@ REQUIRED_KEYS: dict[str, Any] = {
     "EXCLUDE_CHANNELS": bool,
     "MAX_BAD_CHANNELS": int,
     "LONG_CHANNEL_THRESH": float,
-    "PPF": float,
+    "METADATA": dict,
     "DRIFT_MODEL": str,
     "DURATION_BETWEEN_ACTIVITIES": int,
     "HRF_MODEL": str,
@@ -284,8 +285,6 @@ else:
 
 logger = logging.getLogger()
 
-
-
 class ProcessingError(Exception):
     def __init__(self, message: str = "Something went wrong!"):
         self.message = message
@@ -1615,7 +1614,7 @@ def calculate_optical_density(data: BaseRaw, ID: str) -> tuple[BaseRaw, Figure]:
 
 
 # STEP 9: Haemoglobin concentration
-def calculate_haemoglobin_concentration(optical_density_data: BaseRaw, ID: str) -> tuple[BaseRaw, Figure]:
+def calculate_haemoglobin_concentration(optical_density_data: BaseRaw, ID: str, file_path: str) -> tuple[BaseRaw, Figure]:
     """
     Calculates haemoglobin concentration from optical density data using the Beer-Lambert law and generates a plot.
 
@@ -1625,7 +1624,9 @@ def calculate_haemoglobin_concentration(optical_density_data: BaseRaw, ID: str)
         The data in optical density format.
     ID : str
         File name of the the snirf file that was loaded.
-
+    file_path : str
+        Entire file path if snirf file that was loaded.
+        
     Returns
     -------
     tuple[BaseRaw, Figure]
@@ -1636,7 +1637,7 @@ def calculate_haemoglobin_concentration(optical_density_data: BaseRaw, ID: str)
     logger.info("Calculating haemoglobin concentration data...")
         
     # Get the haemoglobin concentration using beer lambert law
-    haemoglobin_concentration_data = beer_lambert_law(optical_density_data, PPF)
+    haemoglobin_concentration_data = beer_lambert_law(optical_density_data, ppf=calculate_dpf(file_path))
 
     logger.info("Creating the figure...")
     fig = cast(Figure, optical_density_data.plot(show=False, n_channels=len(getattr(optical_density_data, "ch_names")), duration=getattr(optical_density_data, "times")[-1]).figure) # type: ignore
@@ -1720,10 +1721,10 @@ def calculate_and_apply_negative_correlation_enhancement(haemoglobin_concentrati
 
 
 
-def calculate_and_apply_short_channel_correction(optical_density_data: BaseRaw) -> dict[str, list[Any] | mne.evoked.EvokedArray]:
+def calculate_and_apply_short_channel_correction(optical_density_data: BaseRaw, file_path: str) -> dict[str, list[Any] | mne.evoked.EvokedArray]:
 
     od_corrected = short_channel_regression(optical_density_data, SHORT_CHANNEL_THRESH)
-    haemoglobin_concentration_data = beer_lambert_law(od_corrected, PPF)
+    haemoglobin_concentration_data = beer_lambert_law(od_corrected, ppf=calculate_dpf(file_path))
     
     events, _ = mne.events_from_annotations(haemoglobin_concentration_data, event_id={"Reach": 1, "Start of Rest": 2}, verbose=VERBOSITY) # type: ignore
     event_dict = {"Reach": 1, "Start of Rest": 2}
@@ -1917,6 +1918,32 @@ def run_GLM_analysis(data: BaseRaw, design_matrix: DataFrame) -> RegressionResul
     return glm_est
 
 
+def calculate_dpf(file_path):
+    # order is hbo / hbr
+    with h5py.File(file_path, 'r') as f:
+        wavelengths = f['/nirs/probe/wavelengths'][:]
+        print("Wavelengths (nm):", wavelengths)
+    wavelengths = sorted(wavelengths, reverse=True)
+    data = METADATA.get(file_path)
+    if data is None:
+        age = 25
+    else:
+        age = data['Age']
+    logger.info(age)
+    age = float(age)
+    a = 223.3
+    b = 0.05624
+    c = 0.8493
+    d = -5.723e-7
+    e = 0.001245
+    f = -0.9025
+    dpf = []
+    for w in wavelengths:
+        logger.info(w)
+        dpf.append(a + b * (age**c) + d* (w**3) + e * (w**2) + f*w)
+    logger.info(dpf)
+    return dpf
+
 
 def individual_GLM_analysis(file_path: str, ID: str, stim_duration: float = 5.0, progress_callback=None) -> tuple[BaseRaw, BaseRaw, DataFrame, DataFrame, DataFrame, DataFrame, dict[str, Figure], str, bool, bool]:
     """
@@ -1971,6 +1998,12 @@ def individual_GLM_analysis(file_path: str, ID: str, stim_duration: float = 5.0,
     # Initalize the participants full layout to be the current data regardless if it will be updated later
     raw_full_layout = data
 
+
+    logger.info(file_path)
+    logger.info(ID)
+    logger.info(METADATA.get(file_path))
+    calculate_dpf(file_path)
+    
     try:
         # Did the user want to load new channel positions from an optode file?
         # STEP 2
@@ -1985,7 +2018,7 @@ def individual_GLM_analysis(file_path: str, ID: str, stim_duration: float = 5.0,
         # but i shouldnt need to do od and bll just check the last three numbers
         temp = data.copy() 
         temp_od = cast(BaseRaw, optical_density(temp, verbose=VERBOSITY))
-        raw_full_layout = beer_lambert_law(temp_od, ppf=PPF)
+        raw_full_layout = beer_lambert_law(temp_od, ppf=calculate_dpf(file_path))
 
         # If specified, apply TDDR to the data
         # STEP 3
@@ -2082,11 +2115,11 @@ def individual_GLM_analysis(file_path: str, ID: str, stim_duration: float = 5.0,
         if SHORT_CHANNEL:
             short_chans_od = cast(BaseRaw, optical_density(short_chans))
             data_recombined = cast(BaseRaw, data.copy().add_channels([short_chans_od])) # type: ignore
-            evoked_dict_corr = calculate_and_apply_short_channel_correction(data_recombined.copy())
+            evoked_dict_corr = calculate_and_apply_short_channel_correction(data_recombined.copy(), file_path)
         
         # Calculate the haemoglobin concentration
         # STEP 9
-        data, fig = calculate_haemoglobin_concentration(data, ID)
+        data, fig = calculate_haemoglobin_concentration(data, ID, file_path)
         order_of_operations += " + Haemoglobin Concentration"
         fig_dict['HaemoglobinConcentration'] = fig
         if progress_callback: progress_callback(9)

main.py

@@ -27,7 +27,7 @@ import psutil
 import requests
 from PySide6.QtWidgets import (
     QApplication, QWidget, QMessageBox, QVBoxLayout, QHBoxLayout, QTextEdit, QScrollArea, QComboBox, QGridLayout,
-    QPushButton, QMainWindow, QFileDialog, QLabel, QLineEdit, QFrame, QSizePolicy
+    QPushButton, QMainWindow, QFileDialog, QLabel, QLineEdit, QFrame, QSizePolicy, QGroupBox
 )
 from PySide6.QtCore import QThread, Signal, Qt, QTimer
 from PySide6.QtGui import QAction, QKeySequence, QIcon, QIntValidator, QDoubleValidator
@@ -114,7 +114,7 @@ SECTIONS = [
     {
         "title": "Haemoglobin Concentration",
         "params": [
-            {"name": "PPF", "default": 0.1, "type": float, "help": "Partial Pathlength Factor."},
+            # Intentionally empty (TODO)
         ]
     },
     {
@@ -128,7 +128,7 @@ SECTIONS = [
     {
         "title": "General Linear Model",
         "params": [
-            {"name": "N_JOBS", "default": 1, "type": int, "help": "Number of jobs for processing."},
+            {"name": "N_JOBS", "default": 1, "type": int, "help": "Number of jobs for GLM processing."},
         ]
     },
         {
@@ -137,6 +137,12 @@ SECTIONS = [
             # Intentionally empty (TODO)
         ]
     },
+    {
+        "title": "Other",
+        "params": [
+            {"name": "MAX_WORKERS", "default": 4, "type": int, "help": "Number of files to process at once."},
+        ]
+    },
 ]
 
 
@@ -403,7 +409,7 @@ class ProgressBubble(QWidget):
         self.setLayout(self.layout)
 
         # Store the file path
-        self.file_path = file_path
+        self.file_path = os.path.normpath(file_path)
 
         self.current_step = 0
         # Make the bubble clickable
@@ -619,6 +625,10 @@ class MainApplication(QMainWindow):
         self.platform_suffix = "-" + PLATFORM_NAME
         self.pending_update_version = None
         self.pending_update_path = None
+        
+        self.file_metadata = {}
+        self.current_file = None
+
 
         # Start local pending update check thread
         self.local_check_thread = LocalPendingUpdateCheckThread(CURRENT_VERSION, self.platform_suffix)
@@ -642,11 +652,51 @@ class MainApplication(QMainWindow):
         left_container.setLayout(left_layout)
         left_container.setMinimumWidth(300)
 
-        # Top left widget (for demo, use QTextEdit)
+        top_left_container = QGroupBox()  # Optional: add a title inside parentheses
+        top_left_container.setTitle("File information")  # Optional visible title
+        top_left_container.setStyleSheet("QGroupBox { font-weight: bold; }")  # Style if needed
+        top_left_container.setSizePolicy(QSizePolicy.Preferred, QSizePolicy.Expanding)
+
+        top_left_layout = QHBoxLayout()
+
+        top_left_container.setLayout(top_left_layout)
+
+        # QTextEdit with fixed height, but only 80% width
         self.top_left_widget = QTextEdit()
-        self.top_left_widget.setReadOnly(True) 
+        self.top_left_widget.setReadOnly(True)
         self.top_left_widget.setPlaceholderText("Click a file below to get started! No files below? Open one using File > Open!")
-        self.top_left_widget.setFixedHeight(250)
+
+        # Add QTextEdit to the layout with a stretch factor
+        top_left_layout.addWidget(self.top_left_widget, stretch=4)  # 80%
+        
+        # Create a vertical box layout for the right 20%
+        self.right_column_widget = QWidget()
+        right_column_layout = QVBoxLayout()
+        self.right_column_widget.setLayout(right_column_layout)
+
+
+        self.meta_fields = {
+            "Age": QLineEdit(),
+            "Gender": QLineEdit(),
+        }
+        
+
+        # Inside your top-left container's right column layout:
+        for key, field in self.meta_fields.items():
+            label = QLabel(key.capitalize())
+            field.setPlaceholderText(f"Enter {key}")
+            right_column_layout.addWidget(label)
+            right_column_layout.addWidget(field)
+
+        right_column_layout.addStretch()  # Push fields to top
+    
+        self.right_column_widget.hide()
+        
+        # Add right column widget to the top-left layout (takes 20% width)
+        top_left_layout.addWidget(self.right_column_widget, stretch=1)
+
+        # Add top_left_container to the main left_layout
+        left_layout.addWidget(top_left_container)
 
         # Bottom left: the bubbles inside a scroll area
         self.bubble_container = QWidget()
@@ -660,7 +710,6 @@ class MainApplication(QMainWindow):
         self.scroll_area.setMinimumHeight(300)
 
         # Add top left and bottom left to left layout
-        left_layout.addWidget(self.top_left_widget)
         left_layout.addWidget(self.scroll_area)
 
         self.progress_update_signal.connect(self.update_file_progress)
@@ -713,6 +762,7 @@ class MainApplication(QMainWindow):
         self.button2.setMinimumSize(100, 40)
         self.button3.setMinimumSize(100, 40)
 
+        self.button1.setVisible(False)
         self.button3.setVisible(False) 
 
         self.button1.clicked.connect(self.on_run_task)
@@ -828,6 +878,8 @@ class MainApplication(QMainWindow):
 
     def clear_all(self):
         
+        self.right_column_widget.hide()
+        
         # Clear the bubble layout
         while self.bubble_layout.count():
             item = self.bubble_layout.takeAt(0)
@@ -846,6 +898,7 @@ class MainApplication(QMainWindow):
         self.all_figures = None
         
         # Reset any visible UI elements
+        self.button1.setVisible(False)
         self.button3.setVisible(False)
         self.top_left_widget.clear()
 
@@ -889,6 +942,8 @@ class MainApplication(QMainWindow):
         if file_path:
             self.selected_path = file_path  # store the file path
             self.show_files_as_bubbles(file_path)
+        
+        self.button1.setVisible(True)
 
     def open_folder_dialog(self):
         folder_path = QFileDialog.getExistingDirectory(
@@ -897,6 +952,8 @@ class MainApplication(QMainWindow):
         if folder_path:
             self.selected_path = folder_path  # store the folder path
             self.show_files_as_bubbles(folder_path)
+        
+        self.button1.setVisible(True)
 
 
     def open_multiple_folders_dialog(self):
@@ -921,6 +978,8 @@ class MainApplication(QMainWindow):
             )
             if more == QMessageBox.StandardButton.No:
                 break
+            
+        self.button1.setVisible(True)
 
     def save_project(self):
 
@@ -990,7 +1049,8 @@ class MainApplication(QMainWindow):
 
             self.show_files_as_bubbles_from_list(data["file_list"], data.get("progress_states", {}), filename)
 
-            # Re-enable the "Viewer" button
+            # Re-enable the buttons
+            self.button1.setVisible(True)
             self.button3.setVisible(True)
 
             QMessageBox.information(self, "Loaded", f"Project loaded from:\n{filename}")
@@ -1089,6 +1149,10 @@ class MainApplication(QMainWindow):
 
 
     def on_bubble_clicked(self, bubble):
+        
+        # show age / gender
+        self.right_column_widget.show()
+        
         file_path = bubble.file_path
         if not os.path.exists(file_path):
             self.top_left_widget.setText("File not found.")
@@ -1098,7 +1162,7 @@ class MainApplication(QMainWindow):
         created = time.ctime(os.path.getctime(file_path))
         modified = time.ctime(os.path.getmtime(file_path))
 
-        # snirf_info = self.get_snirf_metadata_mne(file_path)
+        snirf_info = self.get_snirf_metadata_mne(file_path)
 
         info = f"""\
             File: {os.path.basename(file_path)}
@@ -1108,28 +1172,64 @@ class MainApplication(QMainWindow):
             Full Path: {file_path}
             """
 
-        # if "Error" in snirf_info:
+        if "Error" in snirf_info:
-        #     info += f"\nSNIRF Metadata could not be loaded: {snirf_info['Error']}"
+            info += f"\nSNIRF Metadata could not be loaded: {snirf_info['Error']}"
-        # else:
+        else:
-        #     info += "\nSNIRF Metadata:\n"
+            info += "\nSNIRF Metadata:\n"
-        #     for k, v in snirf_info.items():
+            for k, v in snirf_info.items():
-        #         if isinstance(v, list):
+                if isinstance(v, list):
-        #             info += f"  {k}:\n"
+                    info += f"  {k}:\n"
-        #             for item in v:
+                    for item in v:
-        #                 info += f"    - {item}\n"
+                        info += f"    - {item}\n"
-        #         else:
+                else:
-        #             info += f"  {k}: {v}\n"
+                    info += f"  {k}: {v}\n"
 
         self.top_left_widget.setText(info)
+        
+        clicked_bubble = self.sender()
+        file_path = clicked_bubble.file_path
+
+        # Save current file's metadata
+        if self.current_file:
+            self.save_metadata(self.current_file)
+
+        # Update current file
+        self.current_file = file_path
+
+        # Load new file's metadata into the fields
+        metadata = self.file_metadata.get(file_path, {})
+        for key, field in self.meta_fields.items():
+            field.blockSignals(True)
+            field.setText(metadata.get(key, ""))
+            field.blockSignals(False)
 
     def placeholder(self):
         QMessageBox.information(self, "Placeholder", "This feature is not implemented yet.")
 
+    def save_metadata(self, file_path):
+        if not file_path:
+            return
 
+        self.file_metadata[file_path] = {
+            key: field.text()
+            for key, field in self.meta_fields.items()
+        }
+        
+    def get_all_metadata(self):
+        # First, make sure current file's edits are saved
+        if self.current_file:
+            self.save_metadata(self.current_file)
+
+        return self.file_metadata
 
 
     '''MODULE FILE'''
     def on_run_task(self):
+        
+        all_metadata = self.get_all_metadata()
+
+        for file_path, data in all_metadata.items():
+            print(f"{file_path}: {data}")
 
         collected_data = {}
 
@@ -1164,7 +1264,6 @@ class MainApplication(QMainWindow):
             collected_data["SNIRF_SUBFOLDERS"] = [Path(p).name for p in self.selected_paths]
             collected_data["STIM_DURATION"] = [0 for _ in self.selected_paths]
 
-
         elif hasattr(self, "selected_path") and self.selected_path:
             # Handle single folder
             selected_path = Path(self.selected_path)
@@ -1176,10 +1275,9 @@ class MainApplication(QMainWindow):
             # No folder selected - handle gracefully or raise error
             raise ValueError("No folder(s) selected")
 
-
+        collected_data["METADATA"] = all_metadata
         collected_data["HRF_MODEL"] = 'fir'
 
-        collected_data["MAX_WORKERS"] = 12
         collected_data["FORCE_DROP_CHANNELS"] = []
 
         collected_data["TARGET_ACTIVITY"] = "Reach"
@@ -1445,6 +1543,39 @@ class MainApplication(QMainWindow):
         def normalize(v): return [int(x) for x in v.split(".")]
         return (normalize(v1) > normalize(v2)) - (normalize(v1) < normalize(v2))
 
+    def get_snirf_metadata_mne(self, file_name):
+        import mne
+        from mne.preprocessing.nirs import source_detector_distances
+
+        raw = mne.io.read_raw_snirf(file_name, preload=True)
+
+        snirf_info = {}
+
+        # Measurement date
+        snirf_info['Measurement Date'] = str(raw.info.get('meas_date'))
+
+        # Source-detector distances
+        distances = source_detector_distances(raw.info)
+        distance_info = []
+        for ch_name, dist in zip(raw.info['ch_names'], distances):
+            distance_info.append(f"{ch_name}: {dist:.4f} m")
+        snirf_info['Source-Detector Distances'] = distance_info
+
+        # Digitization points / optode positions
+        dig = raw.info.get('dig', None)
+        if dig is not None:
+            dig_info = []
+            for point in dig:
+                kind = point['kind']
+                ident = point['ident']
+                coord = point['r']
+                dig_info.append(f"Kind: {kind}, ID: {ident}, Coord: {coord}")
+            snirf_info['Digitization Points'] = dig_info
+        else:
+            snirf_info['Digitization Points'] = "Not found"
+            
+        return snirf_info
+
 
     def closeEvent(self, event):
         # Gracefully shut down multiprocessing children