Add elementary support for open datasets and epoch-based analysis wit…

…hout raw data

meggie/actions/epochs_create/configuration.json

@@ -2,5 +2,6 @@
     "id": "epochs_create",
     "name": "Create epochs",
     "entry": "CreateEpochs",
-    "description": "Create a new epoch collection for the current subject."
+    "description": "Create a new epoch collection for the current subject.",
+    "tags": ["raw"]
 }

meggie/actions/raw_event_info/configuration.json

@@ -2,5 +2,6 @@
     "id": "raw_event_info",
     "name": "Event info",
     "entry": "Info",
-    "description": "Extract event information from the raw data."
+    "description": "Extract event information from the raw data.",
+    "tags": ["raw"]
 }

meggie/actions/raw_events_from_annotations/configuration.json

@@ -2,5 +2,6 @@
     "id": "raw_events_from_annotations",
     "name": "Events from annotations",
     "entry": "EventsFromAnnotations",
-    "description": "Create events from annotations for further analysis."
+    "description": "Create events from annotations for further analysis.",
+    "tags": ["raw"]
 }

meggie/actions/raw_filter/configuration.json

@@ -2,5 +2,6 @@
     "id": "raw_filter",
     "name": "Filter",
     "entry": "Filter",
-    "description": "Apply low-pass, high-pass, band-pass, and band-stop filters to raw data to isolate specific frequency ranges or remove unwanted frequencies."
+    "description": "Apply low-pass, high-pass, band-pass, and band-stop filters to raw data to isolate specific frequency ranges or remove unwanted frequencies.",
+    "tags": ["raw"]
 }

meggie/actions/raw_ica/configuration.json

@@ -2,5 +2,6 @@
     "id": "raw_ica",
     "name": "Artifact removal",
     "entry": "ICA",
-    "description": "Apply Independent Component Analysis (ICA) to raw data to identify and remove artifacts such as heartbeats and eye blinks."
+    "description": "Apply Independent Component Analysis (ICA) to raw data to identify and remove artifacts such as heartbeats and eye blinks.",
+    "tags": ["raw"]
 }

meggie/actions/raw_measurement_info/configuration.json

@@ -2,5 +2,6 @@
     "id": "raw_measurement_info",
     "name": "Measurement info",
     "entry": "Info",
-    "description": "Extract measurement information from the raw data."
+    "description": "Extract measurement information from the raw data.",
+    "tags": ["raw"]
 }

meggie/actions/raw_montage/configuration.json

@@ -3,5 +3,5 @@
     "name": "Montage",
     "entry": "Montage",
     "description": "Apply a montage to the EEG dataset, enabling the creation of topographical plots.",
-    "tags": ["eeg"]
+    "tags": ["eeg", "raw"]
 }

meggie/actions/raw_plot/configuration.json

@@ -2,5 +2,6 @@
     "id": "raw_plot",
     "name": "Plot raw",
     "entry": "PlotRaw",
-    "description": "Produce a time series plot of the raw data."
+    "description": "Produce a time series plot of the raw data.",
+    "tags": ["raw"]
 }

meggie/actions/raw_plot_projections/configuration.json

@@ -2,5 +2,6 @@
     "id": "raw_plot_projections",
     "name": "Plot projections",
     "entry": "PlotProjections",
-    "description": "Generate a plot to visualize the projection vectors contained within the raw data."
+    "description": "Generate a plot to visualize the projection vectors contained within the raw data.",
+    "tags": ["raw"]
 }

meggie/actions/raw_rereference/configuration.json

@@ -3,5 +3,5 @@
     "name": "Rereference",
     "entry": "Rereference",
     "description": "Re-reference the raw data to an average reference, which can be computed from one or more selected channels or all channels.",
-    "tags": ["eeg"]
+    "tags": ["eeg", "raw"]
 }

meggie/actions/raw_resample/configuration.json

@@ -2,5 +2,6 @@
     "id": "raw_resample",
     "name": "Resample",
     "entry": "Resample",
-    "description": "Adjust the dataset by resampling it to a different sampling frequency."
+    "description": "Adjust the dataset by resampling it to a different sampling frequency.",
+    "tags": ["raw"]
 }

meggie/actions/spectrum_create/configuration.json

@@ -2,5 +2,6 @@
     "id": "spectrum_create",
     "name": "Create spectrum",
     "entry": "CreateSpectrum",
-    "description": "Calculate the spectral data at specified time intervals for the current subject."
+    "description": "Calculate the spectral data at specified time intervals for the current subject.",
+    "tags": ["raw"]
 }

meggie/experiment.py

@@ -184,7 +184,8 @@ def activate_subject(self, subject_name):
         self.active_subject = self.subjects[subject_name]
 
         # test validity
-        self.active_subject.get_raw(preload=False)
+        if self.active_subject.has_raw:
+            self.active_subject.get_raw(preload=False)
 
         return self.active_subject
 
@@ -196,25 +197,41 @@ def create_subject(self, subject_name, raw_path):
         ----------
         subject_name : str
             Name of the new subject.
-        raw_path : str
+        raw_path : str | None
             Path to the data file.
+
+        Returns
+        -------
+        meggie.subject.Subject
+            The activated subject.
+
         """
-        bname = os.path.basename(raw_path)
-        stem, ext = os.path.splitext(bname)
-        new_fname = stem + ".fif"
 
         uid = generate_uid()
 
-        subject = Subject(self, subject_name, new_fname, uid)
-        subject.ensure_folders()
+        # it is possible to add "placeholder" subjects with only e.g epochs data
+        if raw_path:
+            bname = os.path.basename(raw_path)
+            stem, ext = os.path.splitext(bname)
+            new_fname = stem + ".fif"
 
-        raw = open_raw(raw_path)
+            subject = Subject(self, subject_name, new_fname, uid)
+            subject.ensure_folders()
 
-        new_path = os.path.join(subject.path, new_fname)
-        save_raw(raw, new_path)
+            raw = open_raw(raw_path)
+
+            new_path = os.path.join(subject.path, new_fname)
+            save_raw(raw, new_path)
+
+        else:
+            subject = Subject(self, subject_name, "", uid)
+
+        subject.ensure_folders()
 
         self.add_subject(subject)
 
+        return subject
+
     def save_experiment_settings(self):
         """
         Saves the experiment settings into a file in the root of
@@ -225,7 +242,7 @@ def save_experiment_settings(self):
         for subject in self.subjects.values():
             subject_dict = {
                 "subject_name": subject.name,
-                "raw_fname": subject.raw_fname,
+                "raw_fname": subject.raw_fname if subject.raw_fname else "",
                 "uid": subject.uid,
                 "ica_applied": subject.ica_applied,
                 "rereferenced": subject.rereferenced,
@@ -401,11 +418,10 @@ def open_existing_experiment(prefs, path=None):
         subject_name = subject_data["subject_name"]
 
         raw_fname = subject_data.get("raw_fname")
+
         # for backwards compatibility
         if not raw_fname:
             raw_fname = subject_data.get("working_file_name")
-        if not raw_fname:
-            raise Exception("raw_fname not set in the exp file")
 
         uid = subject_data.get("uid")
         if not uid:

meggie/mainWindowMain.py

@@ -273,18 +273,27 @@ def update_ui(self):
     def reconstruct_tabs(self):
         """Reconstructs the tabs."""
 
-        if self.experiment and self.experiment.active_subject:
-            include_eeg = self.experiment.active_subject.has_eeg
-        else:
-            include_eeg = True
+        include_eeg = True
+        has_raw = True
+        if self.experiment:
+            active_subject = self.experiment.active_subject
+            if active_subject:
+                has_raw = active_subject.has_raw
+                if has_raw:
+                    include_eeg = active_subject.has_eeg
 
         if self.experiment:
             selected_pipeline = self.experiment.selected_pipeline
         else:
             selected_pipeline = "classic"
+
         try:
             self.tabs = construct_tabs(
-                selected_pipeline, self, self.prefs, include_eeg=include_eeg
+                selected_pipeline,
+                self,
+                self.prefs,
+                include_eeg=include_eeg,
+                has_raw=has_raw,
             )
         except Exception as exc:
             self.tabs = []

meggie/mainwindow/dialogs/createExperimentDialogMain.py

@@ -9,6 +9,8 @@
 
 from meggie.mainwindow.dynamic import find_all_package_specs
 
+from meggie.utilities.threading import threaded
+from meggie.utilities.datasets import get_open_datasets
 from meggie.utilities.messaging import exc_messagebox
 from meggie.utilities.messaging import messagebox
 
@@ -27,6 +29,11 @@ def __init__(self, parent):
 
         self.active_plugins = prefs.active_plugins
 
+        self.ui.comboBoxOpenData.addItem("")
+        self.datasets = sorted(get_open_datasets().items(), key=lambda x: x[1]["title"])
+        for key, dataset in self.datasets:
+            self.ui.comboBoxOpenData.addItem(dataset["title"])
+
         # read all pipeline ids and names to a list
         pipelines = []
         package_specs = find_all_package_specs()
@@ -78,12 +85,23 @@ def accept(self):
                 selected_pipeline = self.pipelines[button_idx][0]
                 break
 
+        name = self.ui.lineEditExperimentName.text()
+        author = self.ui.lineEditAuthor.text()
+        prefs = self.parent.prefs
+
         try:
-            experiment = initialize_new_experiment(
-                self.ui.lineEditExperimentName.text(),
-                self.ui.lineEditAuthor.text(),
-                self.parent.prefs,
-            )
+            open_data_index = self.ui.comboBoxOpenData.currentIndex()
+
+            @threaded
+            def threaded_initialize():
+                if open_data_index == 0:
+                    experiment = initialize_new_experiment(name, author, prefs)
+                else:
+                    item = self.datasets[open_data_index - 1]
+                    experiment = item[1]["constructor"](name, author, prefs)
+                return experiment
+
+            experiment = threaded_initialize(do_meanwhile=self.parent.update_ui)
 
             experiment.selected_pipeline = selected_pipeline
             experiment.save_experiment_settings()

meggie/mainwindow/dialogs/createExperimentDialogUi.py

@@ -2,9 +2,10 @@
 
 # Form implementation generated from reading ui file 'createExperimentDialogUi.ui'
 #
-# Created by: PyQt5 UI code generator 5.12.3
+# Created by: PyQt5 UI code generator 5.15.9
 #
-# WARNING! All changes made in this file will be lost!
+# WARNING: Any manual changes made to this file will be lost when pyuic5 is
+# run again.  Do not edit this file unless you know what you are doing.
 
 
 from PyQt5 import QtCore, QtWidgets
@@ -27,10 +28,6 @@ def setupUi(self, CreateExperimentDialog):
         self.scrollAreaWidgetContents.setObjectName("scrollAreaWidgetContents")
         self.gridLayout = QtWidgets.QGridLayout(self.scrollAreaWidgetContents)
         self.gridLayout.setObjectName("gridLayout")
-        spacerItem = QtWidgets.QSpacerItem(
-            20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding
-        )
-        self.gridLayout.addItem(spacerItem, 2, 1, 1, 1)
         self.groupBoxInfo = QtWidgets.QGroupBox(self.scrollAreaWidgetContents)
         self.groupBoxInfo.setObjectName("groupBoxInfo")
         self.gridLayout_2 = QtWidgets.QGridLayout(self.groupBoxInfo)
@@ -53,6 +50,21 @@ def setupUi(self, CreateExperimentDialog):
         self.gridLayoutPipeline = QtWidgets.QGridLayout(self.groupBoxPipeline)
         self.gridLayoutPipeline.setObjectName("gridLayoutPipeline")
         self.gridLayout.addWidget(self.groupBoxPipeline, 1, 1, 1, 1)
+        spacerItem = QtWidgets.QSpacerItem(
+            20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding
+        )
+        self.gridLayout.addItem(spacerItem, 3, 1, 1, 1)
+        self.groupBoxOpenData = QtWidgets.QGroupBox(self.scrollAreaWidgetContents)
+        self.groupBoxOpenData.setObjectName("groupBoxOpenData")
+        self.gridLayout_4 = QtWidgets.QGridLayout(self.groupBoxOpenData)
+        self.gridLayout_4.setObjectName("gridLayout_4")
+        self.labelOpenData = QtWidgets.QLabel(self.groupBoxOpenData)
+        self.labelOpenData.setObjectName("labelOpenData")
+        self.gridLayout_4.addWidget(self.labelOpenData, 0, 0, 1, 1)
+        self.comboBoxOpenData = QtWidgets.QComboBox(self.groupBoxOpenData)
+        self.comboBoxOpenData.setObjectName("comboBoxOpenData")
+        self.gridLayout_4.addWidget(self.comboBoxOpenData, 0, 1, 1, 1)
+        self.gridLayout.addWidget(self.groupBoxOpenData, 2, 1, 1, 1)
         self.scrollArea.setWidget(self.scrollAreaWidgetContents)
         self.gridLayout_3.addWidget(self.scrollArea, 0, 0, 1, 1)
         self.horizontalLayoutButtons = QtWidgets.QHBoxLayout()
@@ -70,8 +82,8 @@ def setupUi(self, CreateExperimentDialog):
         self.gridLayout_3.addLayout(self.horizontalLayoutButtons, 2, 0, 1, 1)
 
         self.retranslateUi(CreateExperimentDialog)
-        self.pushButtonAccept.clicked.connect(CreateExperimentDialog.accept)
-        self.pushButtonCancel.clicked.connect(CreateExperimentDialog.reject)
+        self.pushButtonAccept.clicked.connect(CreateExperimentDialog.accept)  # type: ignore
+        self.pushButtonCancel.clicked.connect(CreateExperimentDialog.reject)  # type: ignore
         QtCore.QMetaObject.connectSlotsByName(CreateExperimentDialog)
 
     def retranslateUi(self, CreateExperimentDialog):
@@ -91,5 +103,9 @@ def retranslateUi(self, CreateExperimentDialog):
         self.groupBoxPipeline.setTitle(
             _translate("CreateExperimentDialog", "Select a pipeline for the analysis:")
         )
+        self.groupBoxOpenData.setTitle(
+            _translate("CreateExperimentDialog", "Create from open data:")
+        )
+        self.labelOpenData.setText(_translate("CreateExperimentDialog", "Dataset:"))
         self.pushButtonCancel.setText(_translate("CreateExperimentDialog", "Cancel"))
         self.pushButtonAccept.setText(_translate("CreateExperimentDialog", "Ok"))

meggie/mainwindow/dialogs/createExperimentDialogUi.ui

@@ -41,19 +41,6 @@
        </size>
       </property>
       <layout class="QGridLayout" name="gridLayout">
-       <item row="2" column="1">
-        <spacer name="verticalSpacer">
-         <property name="orientation">
-          <enum>Qt::Vertical</enum>
-         </property>
-         <property name="sizeHint" stdset="0">
-          <size>
-           <width>20</width>
-           <height>40</height>
-          </size>
-         </property>
-        </spacer>
-       </item>
        <item row="0" column="1">
         <widget class="QGroupBox" name="groupBoxInfo">
          <property name="title">
@@ -91,6 +78,38 @@
          <layout class="QGridLayout" name="gridLayoutPipeline"/>
         </widget>
        </item>
+       <item row="3" column="1">
+        <spacer name="verticalSpacer">
+         <property name="orientation">
+          <enum>Qt::Vertical</enum>
+         </property>
+         <property name="sizeHint" stdset="0">
+          <size>
+           <width>20</width>
+           <height>40</height>
+          </size>
+         </property>
+        </spacer>
+       </item>
+       <item row="2" column="1">
+        <widget class="QGroupBox" name="groupBoxOpenData">
+         <property name="title">
+          <string>Create from open data:</string>
+         </property>
+         <layout class="QGridLayout" name="gridLayout_4">
+          <item row="0" column="0">
+           <widget class="QLabel" name="labelOpenData">
+            <property name="text">
+             <string>Dataset:</string>
+            </property>
+           </widget>
+          </item>
+          <item row="0" column="1">
+           <widget class="QComboBox" name="comboBoxOpenData"/>
+          </item>
+         </layout>
+        </widget>
+       </item>
       </layout>
      </widget>
     </widget>