ENH: Nodes and Redesign

.pre-commit-config.yaml

@@ -22,3 +22,10 @@ repos:
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
+
+  # docformatter
+  - repo: https://github.com/PyCQA/docformatter
+    rev: eb1df347edd128b30cd3368dddc3aa65edcfac38
+    hooks:
+      - id: docformatter
+        additional_dependencies: [ tomli ]

README.md

@@ -99,6 +99,7 @@ The colorpalettes for light and dark theme are inspired from [PyQtDarkTheme](htt
 Many ideas and basics for GUI-Programming where taken
 from [LearnPyQt](https://www.learnpyqt.com/) and numerous
 stackoverflow-questions/solutions.
+For the nodes, code and major influences from [NodeGraphQt](https://github.com/jchanvfx/NodeGraphQt) are used.
 
 The development is financially supported
 by [Heidelberg University](https://www.uni-heidelberg.de/de/forschung/forschungsprofil/fields-of-focus/field-of-focus-i).

mne_pipeline_hd/conftest.py

@@ -8,8 +8,9 @@
 
 import pytest
 
+from mne_pipeline_hd.gui.node.node_viewer import NodeViewer
 from mne_pipeline_hd.gui.main_window import MainWindow
-from mne_pipeline_hd.pipeline.controller import Controller
+from mne_pipeline_hd.pipeline.controller import Controller, NewController
 from mne_pipeline_hd.pipeline.pipeline_utils import _set_test_run
 
 
@@ -32,3 +33,58 @@ def main_window(controller, qtbot):
     qtbot.addWidget(mw)
 
     return mw
+
+
+@pytest.fixture
+def nodeviewer(qtbot):
+    viewer = NodeViewer(NewController(), debug_mode=True)
+    viewer.resize(1000, 1000)
+    qtbot.addWidget(viewer)
+    viewer.show()
+
+    func_kwargs = {
+        "ports": [
+            {
+                "name": "In1",
+                "port_type": "in",
+                "accepted_ports": ["Out1"],
+            },
+            {
+                "name": "In2",
+                "port_type": "in",
+                "accepted_ports": ["Out1, Out2"],
+            },
+            {
+                "name": "Out1",
+                "port_type": "out",
+                "accepted_ports": ["In1"],
+                "multi_connection": True,
+            },
+            {
+                "name": "Out2",
+                "port_type": "out",
+                "accepted_ports": ["In1", "In2"],
+                "multi_connection": True,
+            },
+        ],
+        "name": "test_func",
+        "parameters": {
+            "low_cutoff": {
+                "alias": "Low-Cutoff",
+                "gui": "FloatGui",
+                "default": 0.1,
+            },
+            "high_cutoff": {
+                "alias": "High-Cutoff",
+                "gui": "FloatGui",
+                "default": 0.2,
+            },
+        },
+    }
+    func_node1 = viewer.create_node("FunctionNode", **func_kwargs)
+    func_node2 = viewer.create_node("FunctionNode", **func_kwargs)
+    func_node1.output(port_idx=0).connect_to(func_node2.input(port_idx=0))
+
+    func_node2.setPos(400, 100)
+
+    return viewer

mne_pipeline_hd/development/animation_test.py

@@ -0,0 +1,50 @@
+# -*- coding: utf-8 -*-
+import sys
+from qtpy.QtWidgets import (
+    QApplication,
+    QGraphicsPathItem,
+    QGraphicsView,
+    QGraphicsScene,
+)
+from qtpy.QtGui import QPen, QColor, QPainterPath
+from qtpy.QtCore import Qt, QVariantAnimation
+
+
+class Edge(QGraphicsPathItem):
+    def __init__(self):
+        super().__init__()
+        self.setPen(QPen(Qt.white, 5, Qt.SolidLine))
+
+        self.animation = QVariantAnimation()
+        self.animation.setLoopCount(-1)
+        self.animation.valueChanged.connect(self.handle_valueChanged)
+        self.animation.setStartValue(QColor("blue"))
+        self.animation.setKeyValueAt(0.25, QColor("green"))
+        self.animation.setKeyValueAt(0.5, QColor("yellow"))
+        self.animation.setKeyValueAt(0.75, QColor("red"))
+        self.animation.setEndValue(QColor("blue"))
+        self.animation.setDuration(2000)
+
+    def start_animation(self):
+        self.animation.start()
+
+    def handle_valueChanged(self, value):
+        pen = self.pen()
+        pen.setColor(value)
+        self.setPen(pen)
+
+
+app = QApplication(sys.argv)
+viewer = QGraphicsView()
+scene = QGraphicsScene()
+viewer.setScene(scene)
+edge = Edge()
+scene.addItem(edge)
+path = QPainterPath()
+path.moveTo(0, 0)
+path.lineTo(100, 100)
+edge.setPath(path)
+edge.start_animation()
+viewer.show()
+
+sys.exit(app.exec())

mne_pipeline_hd/development/development_considerations.md

@@ -48,3 +48,11 @@ setting should be device/OS-dependent:
 2. QSettings(), which is stored by Qt on an OS-depending location and which may
    differ between devices/OS. Settings which dependent on the device/OS should
    go here (e.g. `n_jobs` or `use_cuda`)
+
+## Nodes
+Nodes should improve usability and the representation of the pipeline by the following:
+- The order of execution is now clearer and renders the function-dependency considerations obsolete.
+- The user can now see the input and output of each function.
+- Parameters will now go to each function directly, overview only optional
+- Using multiple File-Lists or Projets side-by-side will be more easy to handle.
+-

mne_pipeline_hd/extra/parameters.csv

@@ -78,7 +78,7 @@ stc_animation_span;;Inverse;(0,0.5);s;time-span for stc-animation[s];TupleGui;
 stc_animation_dilat;;Inverse;20;;time-dilation for stc-animation;IntGui;
 target_labels;Target Labels;Inverse;[];;;LabelGui;
 label_colors;;Inverse;{};;Set custom colors for labels.;ColorGui;{'keys': 'target_labels', 'none_select':True}
-extract_mode;Label-Extraction-Mode;Inverse;auto;;mode for extracting label-time-course from Source-Estimate;ComboGui;{'options': ['auto', 'max', 'mean', 'mean_flip', 'pca_flip']}
+extract_mode;Label-Extraction-Mode;Inverse;mean;;mode for extracting label-time-course from Source-Estimate;ComboGui;{'options': ['auto', 'max', 'mean', 'mean_flip', 'pca_flip']}
 con_methods;;Connectivity;['coh'];;methods for connectivity;CheckListGui;{'options': ['coh', 'cohy', 'imcoh', 'plv', 'ciplv', 'ppc', 'pli', 'pli2_unbiased', 'wpli', 'wpli2_debiased']}
 con_fmin;;Connectivity;30;;lower frequency/frequencies for connectivity;MultiTypeGui;{'type_selection': True, 'types': ['float', 'list']}
 con_fmax;;Connectivity;80;;upper frequency/frequencies for connectivity;MultiTypeGui;{'type_selection': True, 'types': ['float', 'list']}

mne_pipeline_hd/functions/operations.py

@@ -893,8 +893,6 @@ def tfr(
     powers = list()
     itcs = list()
 
-    meeg.load_epochs()
-
     # Calculate Time-Frequency for each trial from epochs
     # using the selected method
     for trial, epoch in meeg.get_trial_epochs():

mne_pipeline_hd/functions/plot.py

@@ -370,7 +370,7 @@ def plot_compare_evokeds(meeg, show_plots):
 
     evokeds = {f"{evoked.comment}={evoked.nave}": evoked for evoked in evokeds}
 
-    fig = mne.viz.plot_compare_evokeds(evokeds, show=show_plots)
+    fig = mne.viz.plot_compare_evokeds(evokeds, title=meeg.name, show=show_plots)
 
     meeg.plot_save("evokeds", subfolder="compare", matplotlib_figure=fig)
 

mne_pipeline_hd/gui/base_widgets.py

@@ -139,11 +139,11 @@ def _data_changed(self, index, _):
         logger().debug(f"{data} changed at {index}")
 
     def content_changed(self):
-        """Informs ModelView about external change made in data"""
+        """Informs ModelView about external change made in data."""
         self.model.layoutChanged.emit()
 
     def replace_data(self, new_data):
-        """Replaces model._data with new_data"""
+        """Replaces model._data with new_data."""
         self.model._data = new_data
         self.content_changed()
 
@@ -431,30 +431,29 @@ def _checked_changed(self):
         logger().debug(f"Changed values: {self.model._checked}")
 
     def replace_checked(self, new_checked):
-        """Replaces model._checked with new checked list"""
+        """Replaces model._checked with new checked list."""
         self.model._checked = new_checked
         self.content_changed()
 
     def select_all(self):
-        """Select all Items while leaving reference to model._checked intact"""
+        """Select all Items while leaving reference to model._checked intact."""
         for item in [i for i in self.model._data if i not in self.model._checked]:
             self.model._checked.append(item)
         # Inform Model about changes
         self.content_changed()
         self._checked_changed()
 
     def clear_all(self):
-        """Deselect all Items while leaving reference
-        to model._checked intact"""
+        """Deselect all Items while leaving reference to model._checked intact."""
         self.model._checked.clear()
         # Inform Model about changes
         self.content_changed()
         self._checked_changed()
 
 
 class CheckDictList(BaseList):
-    """A List-Widget to display the items of a list and mark them depending on
-    their appearance in check_dict.
+    """A List-Widget to display the items of a list and mark them depending on their
+    appearance in check_dict.
 
     Parameters
     ----------
@@ -512,15 +511,15 @@ def __init__(
         )
 
     def replace_check_dict(self, new_check_dict=None):
-        """Replaces model.check_dict with new check_dict"""
+        """Replaces model.check_dict with new check_dict."""
         if new_check_dict:
             self.model._check_dict = new_check_dict
         self.content_changed()
 
 
 class CheckDictEditList(EditList):
-    """A List-Widget to display the items of a list and mark them
-    depending of their appearance in check_dict.
+    """A List-Widget to display the items of a list and mark them depending of their
+    appearance in check_dict.
 
     Parameters
     ----------
@@ -589,7 +588,7 @@ def __init__(
         )
 
     def replace_check_dict(self, new_check_dict=None):
-        """Replaces model.check_dict with new check_dict"""
+        """Replaces model.check_dict with new check_dict."""
         if new_check_dict:
             self.model._check_dict = new_check_dict
         self.content_changed()
@@ -616,10 +615,9 @@ def __init__(
             model.layoutChanged.emit()
 
     def get_keyvalue_by_index(self, index):
-        """For the given index, make an entry in item_dict with the data
-         at index as key and a dict as value defining.
-        if data is key or value and refering to the corresponding key/value
-         of data depending on its type.
+        """For the given index, make an entry in item_dict with the data at index as key
+        and a dict as value defining. if data is key or value and refering to the
+        corresponding key/value of data depending on its type.
 
         Parameters
         ----------
@@ -683,7 +681,7 @@ def select(self, keys, values, clear_selection=True):
 
 
 class SimpleDict(BaseDict):
-    """A Widget to display a Dictionary
+    """A Widget to display a Dictionary.
 
     Parameters
     ----------
@@ -699,7 +697,6 @@ class SimpleDict(BaseDict):
         Set True to resize the rows to contents.
     resize_columns : bool
         Set True to resize the columns to contents.
-
     """
 
     def __init__(
@@ -723,8 +720,9 @@ def __init__(
 
 
 # ToDo: DataChanged somehow not emitted when row is removed
+# ToDo: Bug when removing multiple rows (fix and add tests)
 class EditDict(BaseDict):
-    """A Widget to display and edit a Dictionary
+    """A Widget to display and edit a Dictionary.
 
     Parameters
     ----------
@@ -745,7 +743,6 @@ class EditDict(BaseDict):
         Set True to resize the rows to contents.
     resize_columns : bool
         Set True to resize the columns to contents.
-
     """
 
     def __init__(
@@ -831,8 +828,7 @@ def edit_item(self):
 
 
 class BasePandasTable(Base):
-    """
-    The Base-Class for a table from a pandas DataFrame
+    """The Base-Class for a table from a pandas DataFrame.
 
     Parameters
     ----------
@@ -870,7 +866,7 @@ def __init__(
             model.layoutChanged.emit()
 
     def get_rowcol_by_index(self, index, data_list):
-        """Get the data at index and the row and column of this data
+        """Get the data at index and the row and column of this data.
 
         Parameters
         ----------
@@ -883,7 +879,6 @@ def get_rowcol_by_index(self, index, data_list):
         -----
         Because this function is supposed to be called consecutively,
         the information is stored in an existing list (data_list)
-
         """
         data = self.model.getData(index)
         row = self.model.headerData(
@@ -928,9 +923,7 @@ def _selection_changed(self):
         logger().debug(f"Selection changed to {selection_list}")
 
     def select(self, values=None, rows=None, columns=None, clear_selection=True):
-        """
-        Select items in Pandas DataFrame by value
-        or select complete rows/columns.
+        """Select items in Pandas DataFrame by value or select complete rows/columns.
 
         Parameters
         ----------
@@ -942,7 +935,6 @@ def select(self, values=None, rows=None, columns=None, clear_selection=True):
             Names of columns.
         clear_selection: bool | None
             Set True if you want to clear the selection before selecting.
-
         """
         indexes = list()
         # Get indexes for matching items in pd_data
@@ -980,7 +972,7 @@ def select(self, values=None, rows=None, columns=None, clear_selection=True):
 
 
 class SimplePandasTable(BasePandasTable):
-    """A Widget to display a pandas DataFrame
+    """A Widget to display a pandas DataFrame.
 
     Parameters
     ----------
@@ -1024,7 +1016,7 @@ def __init__(
 
 
 class EditPandasTable(BasePandasTable):
-    """A Widget to display and edit a pandas DataFrame
+    """A Widget to display and edit a pandas DataFrame.
 
     Parameters
     ----------
@@ -1148,8 +1140,8 @@ def init_ui(self):
             self.setLayout(layout)
 
     def update_data(self):
-        """Has to be called, when model._data is rereferenced
-         by for example add_row to keep external data updated.
+        """Has to be called, when model._data is rereferenced by for example add_row to
+        keep external data updated.
 
         Returns
         -------
@@ -1319,7 +1311,7 @@ def closeEvent(self, event):
 
 
 class AssignWidget(QWidget):
-    """ """
+    """"""
 
     def __init__(
         self,