xarray-graph 0.2.1__tar.gz → 0.2.3__tar.gz

{xarray_graph-0.2.1 → xarray_graph-0.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: xarray-graph
-Version: 0.2.1
+Version: 0.2.3
 Summary: PyQt/PySide UI for graphing (x,y) slices of Xarray datasets.
 Keywords: PyQt,PySide,xarray,graph
 Home-page: https://github.com/marcel-goldschen-ohm/xarray-graph
@@ -22,9 +22,9 @@ Requires-Dist: numpy>=1.26.2
 Requires-Dist: xarray>=2023.12.0
 Requires-Dist: qtpy>=2.4.1
 Requires-Dist: qtawesome>=1.3.0
-Requires-Dist: pyqt-ext>=1.2.0
+Requires-Dist: pyqt-ext>=1.2.1
 Requires-Dist: pyqtgraph-ext>=1.2.0
-Requires-Dist: xarray-treeview>=1.2.0
+Requires-Dist: xarray-treeview>=1.2.2
 Requires-Dist: scipy>=1.11.4
 Requires-Dist: lmfit>=1.2.2
 Description-Content-Type: text/markdown

{xarray_graph-0.2.1 → xarray_graph-0.2.3}/pyproject.toml

@@ -11,9 +11,9 @@ dependencies = [
     "xarray>=2023.12.0",
     "qtpy>=2.4.1",
     "qtawesome>=1.3.0",
-    "pyqt-ext>=1.2.0",
+    "pyqt-ext>=1.2.1",
     "pyqtgraph-ext>=1.2.0",
-    "xarray-treeview>=1.2.0",
+    "xarray-treeview>=1.2.2",
     "scipy>=1.11.4",
     "lmfit>=1.2.2",
 ]
@@ -35,7 +35,7 @@ classifiers = [
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
 ]
-version = "0.2.1"
+version = "0.2.3"
 
 [project.license]
 text = "MIT"

{xarray_graph-0.2.1 → xarray_graph-0.2.3}/src/xarray_graph/XarrayGraph.py

@@ -42,11 +42,6 @@ from xarray_treeview import *
 # version info (stored in metadata in case needed later)
 from importlib.metadata import version
 XARRAY_GRAPH_VERSION = version('xarray-graph')
-try:
-    i = re.search(r'[a-zA-Z]', XARRAY_GRAPH_VERSION).start()
-    XARRAY_GRAPH_VERSION = XARRAY_GRAPH_VERSION[:i].rstrip('.')
-except Exception:
-    pass
 
 
 # Currently, color is handled by the widgets themselves.
@@ -120,16 +115,16 @@ class XarrayGraph(QMainWindow):
             if data is None:
                 data = DataTree()
             elif isinstance(data, xr.Dataset):
-                data = DataTree(ds=data)
+                data = DataTree(data=data)
             elif isinstance(data, xr.DataArray):
-                data = DataTree(ds=xr.Dataset(data_vars={data.name: data}))
+                data = DataTree(data=xr.Dataset(data_vars={data.name: data}))
             elif isinstance(data, np.ndarray):
-                data = DataTree(ds=xr.Dataset(data_vars={'data': data}))
+                data = DataTree(data=xr.Dataset(data_vars={'data': data}))
             else:
                 # assume list or tuple of two np.ndarrays (x, y)
                 try:
                     x, y = data
-                    data = DataTree(ds=xr.Dataset(data_vars={'y': ('x', y)}, coords={'x': ('x', x)}))
+                    data = DataTree(data=xr.Dataset(data_vars={'y': ('x', y)}, coords={'x': ('x', x)}))
                 except Exception:
                     raise ValueError('XarrayGraph.data.setter: Invalid input.')
         
@@ -151,6 +146,12 @@ class XarrayGraph(QMainWindow):
         # metadata
         self.attrs['xarray-graph-version'] = XARRAY_GRAPH_VERSION
 
+        # regions tree view
+        self._region_treeview.model().setRoot(AxisRegionTreeItem(self.regions))
+
+        # notes
+        self._notes_edit.setPlainText(self.attrs.get('notes', ''))
+
         # populate array math selections
         # self._update_array_math_comboboxes()
     
@@ -277,7 +278,7 @@ class XarrayGraph(QMainWindow):
             filepath = QFileDialog.getExistingDirectory(self, 'Open from Xarray data store...')
             if filepath == '':
                 return None
-        self.data = open_datatree(filepath)
+        self.data = open_datatree(filepath, 'zarr')
         self._filepath = filepath
         self.setWindowTitle(os.path.split(filepath)[1])
     
@@ -297,31 +298,20 @@ class XarrayGraph(QMainWindow):
         self.setWindowTitle(os.path.split(filepath)[1])
     
     def import_data(self, filepath: str = '', filetype: str = '') -> None:
-        # ds: xr.Dataset | None = None
-        # if filetype == 'pCLAMP':
-        #     # TODO: implement
-        #     QMessageBox.warning(self, 'Import pCLAMP', 'Importing pCLAMP files is not yet implemented.')
-        #     return
-        # elif filetype == 'HEKA':
-        #     # TODO: implement
-        #     QMessageBox.warning(self, 'Import HEKA', 'Importing HEKA files is not yet implemented.')
-        #     return
-        # elif filetype == 'GOLab TEVC':
-        #     ds, filepath = import_golab_tevc(filepath)
-        # if ds is None:
-        #     return
-        # self.set_data(ds)
-        # if 'regions' in ds.attrs:
-        #     self.metadata['regions'] = ds.attrs['regions']
-        #     del ds.attrs['regions']
-        #     region_labels = [region['label'] for region in self.metadata['regions']]
-        #     self._region_label_list.clear()
-        #     self._region_label_list.addItems(region_labels)
-        #     self.set_selected_region_labels(region_labels)
-        # if 'notes' in ds.attrs:
-        #     self.metadata['notes'] = ds.attrs['notes']
-        #     del ds.attrs['notes']
-        #     self.load_notes(self.metadata['notes'])
+        ds: xr.Dataset | None = None
+        if filetype == 'pCLAMP':
+            # TODO: implement
+            QMessageBox.warning(self, 'Import pCLAMP', 'Importing pCLAMP files is not yet implemented.')
+            return
+        elif filetype == 'HEKA':
+            # TODO: implement
+            QMessageBox.warning(self, 'Import HEKA', 'Importing HEKA files is not yet implemented.')
+            return
+        elif filetype == 'GOLab TEVC':
+            ds, filepath = import_golab_tevc(filepath)
+        if ds is None:
+            return
+        self.data = ds
         self._filepath = os.path.splitext(filepath)[0]
         self.setWindowTitle(os.path.split(filepath)[1])
     
@@ -915,8 +905,9 @@ class XarrayGraph(QMainWindow):
             item.deleteLater()
             self.add_region(region)
             
-            # stop drawing regions (draw one at a time)
-            self._set_region_drawing_mode(False)
+            # stop drawing regions (draw one at a time)?
+            if self._draw_single_region_action.isChecked():
+                self._set_region_drawing_mode(False)
 
     def _setup_ui(self) -> None:
         self._setup_menubar()
@@ -926,11 +917,13 @@ class XarrayGraph(QMainWindow):
         self._control_panel_toolbar.setStyleSheet("QToolBar{spacing:2px;}")
         self._control_panel_toolbar.setIconSize(QSize(DEFAULT_ICON_SIZE, DEFAULT_ICON_SIZE))
         self._control_panel_toolbar.setMovable(False)
+        self._control_panel_toolbar.setContextMenuPolicy(Qt.ContextMenuPolicy.PreventContextMenu)
 
         self._plot_grid_toolbar = QToolBar()
         self._plot_grid_toolbar.setStyleSheet("QToolBar{spacing:2px;}")
         self._plot_grid_toolbar.setIconSize(QSize(DEFAULT_ICON_SIZE, DEFAULT_ICON_SIZE))
         self._plot_grid_toolbar.setMovable(False)
+        self._plot_grid_toolbar.setContextMenuPolicy(Qt.ContextMenuPolicy.PreventContextMenu)
         icon_button = QToolButton()
         icon_button.setIcon(qta.icon('fa5s.cubes', options=[{'opacity': 0.5}]))
         icon_button.pressed.connect(self.refresh)
@@ -1001,6 +994,18 @@ class XarrayGraph(QMainWindow):
         self._region_button.clicked.connect(self._set_region_drawing_mode)
         self._action_after_dim_iter_things = self._plot_grid_toolbar.addWidget(self._region_button)
 
+        self._region_button_menu = QMenu()
+        self._draw_single_region_action = QAction('Draw single region', self._region_button_menu, checkable=True, checked=True)
+        self._draw_multiple_regions_action = QAction('Draw multiple regions', self._region_button_menu, checkable=True, checked=False)
+        self._region_button_menu.addAction(self._draw_single_region_action)
+        self._region_button_menu.addAction(self._draw_multiple_regions_action)
+        group = QActionGroup(self._region_button_menu)
+        group.addAction(self._draw_single_region_action)
+        group.addAction(self._draw_multiple_regions_action)
+        group.setExclusive(True)
+        self._region_button.setContextMenuPolicy(Qt.ContextMenuPolicy.CustomContextMenu)
+        self._region_button.customContextMenuRequested.connect(lambda pos: self._region_button_menu.exec_(self._region_button.mapToGlobal(pos)))
+
         self._home_button = QToolButton()
         self._home_button.setIcon(qta.icon('mdi.home-outline', options=[{'opacity': 0.5}]))
         self._home_button.setToolTip('Autoscale all plots')
@@ -1054,7 +1059,8 @@ class XarrayGraph(QMainWindow):
         button.released.connect(lambda i=self._control_panel.count(): self._toggle_control_panel_at(i))
         self._control_panel_toolbar.addWidget(button)
 
-        self._data_treeview = XarrayTreeView()
+        self._data_treeviewer = XarrayTreeViewer()
+        self._data_treeview = self._data_treeviewer.view()
         self._data_treeview.setSelectionMode(QAbstractItemView.SelectionMode.ExtendedSelection)
         root: XarrayTreeItem = XarrayTreeItem(node=self.data, key=None)
         model: XarrayTreeModel = XarrayTreeModel(root)
@@ -1062,6 +1068,7 @@ class XarrayGraph(QMainWindow):
         self._data_treeview.setShowCoords(False)
         self._data_treeview.setModel(model)
         self._data_treeview.selectionWasChanged.connect(self._on_tree_selection_changed)
+        self._data_treeviewer.setSizes([100, 1])
 
         self._xdim_combobox = QComboBox()
         self._xdim_combobox.currentTextChanged.connect(self.set_xdim)
@@ -1071,7 +1078,7 @@ class XarrayGraph(QMainWindow):
         vbox.setContentsMargins(0, 0, 0, 0)
         vbox.setSpacing(0)
 
-        vbox.addWidget(self._data_treeview)
+        vbox.addWidget(self._data_treeviewer)
 
         form = QFormLayout()
         form.setContentsMargins(5, 3, 0, 3)
@@ -1505,6 +1512,13 @@ class XarrayGraph(QMainWindow):
 
         self._control_panel.addWidget(scroll_area)
     
+    # def _show_region_context_menu(self, pos: QPoint) -> None:
+    #     if not hasattr(self, '_region_button_menu'):
+    #         self._region_button_menu = QMenu()
+    #     menu = QMenu()
+    #     menu.addAction('Draw X-axis regions until unchecked', self.clear_regions)
+    #     menu.exec(self.sender().mapToGlobal(pos))
+    
     def _set_region_drawing_mode(self, draw: bool | None = None) -> None:
         if draw is None:
             draw = self._region_button.isChecked()
@@ -1733,7 +1747,7 @@ class XarrayGraph(QMainWindow):
                 i = np.argpartition(x, len(x) // 2)[len(x) // 2]
                 return x[i]
         if measure_type in ['Min', 'Max', 'AbsMax', 'Peaks']:
-            peak_width = self._peak_width_spinbox.value()
+            peak_width = self._peak_half_width_spinbox.value()
             if peak_width > 0:
                 def get_peak_index_range(mask, center_index):
                     start, stop = center_index, center_index + 1
@@ -2018,21 +2032,21 @@ class XarrayGraph(QMainWindow):
                 dims = yarr.dims
                 
                 # region mask for fit optimization and/or evaluation
-                if regions and (self._curve_fit_optimize_in_visible_regions_checkbox.isChecked() or self._curve_fit_evaluate_in_visible_regions_checkbox.isChecked()):
+                if regions and (self._curve_fit_optimize_in_regions_checkbox.isChecked() or self._curve_fit_evaluate_in_regions_checkbox.isChecked()):
                     # mask for combined regions
                     regions_mask = np.full(xdata.shape, False)
                     for region in regions:
                         xmin, xmax = region
                         regions_mask[(xdata >= xmin) & (xdata <= xmax)] = True
 
-                if regions and self._curve_fit_optimize_in_visible_regions_checkbox.isChecked():
+                if regions and self._curve_fit_optimize_in_regions_checkbox.isChecked():
                     xinput = xdata[regions_mask]
                     yinput = ydata[regions_mask]
                 else:
                     xinput = xdata
                     yinput = ydata
 
-                if regions and self._curve_fit_evaluate_in_visible_regions_checkbox.isChecked():
+                if regions and self._curve_fit_evaluate_in_regions_checkbox.isChecked():
                     xoutput = xdata[regions_mask]
                 else:
                     xoutput = xdata
@@ -2207,43 +2221,41 @@ def permutations(coords: dict) -> list[dict]:
     return permutations
 
 
-# def import_golab_tevc(filepath: str = '', parent: QWidget = None) -> tuple[xr.Dataset, str]:
-#     if filepath == '':
-#         filepath, _filter = QFileDialog.getOpenFileName(parent, 'Import GoLab TEVC', '', 'GoLab TEVC (*.mat)')
-#         if filepath == '':
-#             return None
-#     matdict = sp.io.loadmat(filepath, simplify_cells=True)
-#     # print(matdict)
-#     current = matdict['current']
-#     current_units = matdict['current_units']
-#     if len(current_units) > 1:
-#         prefix = current_units[0]
-#         if prefix in metric_scale_factors:
-#             current *= metric_scale_factors[prefix]
-#             current_units = current_units[1:]
-#     time = np.arange(len(current)) * matdict['time_interval_sec']
-#     ds = xr.Dataset(
-#         data_vars={
-#             'current': (['time'], current, {'units': current_units}),
-#         },
-#         coords={
-#             'time': (['time'], time, {'units': 's'}),
-#         },
-#     )
-#     if 'events' in matdict and matdict['events']:
-#         ds.attrs['regions'] = []
-#         for event in matdict['events']:
-#             time = event['time_sec']
-#             text = event['text']
-#             ds.attrs['regions'].append({
-#                 'dim': 'time',
-#                 'label': f'{time:.6f}',
-#                 'region': [time, time],
-#                 'text': text,
-#             })
-#     if 'notes' in matdict:
-#         ds.attrs['notes'] = matdict['notes']
-#     return ds, filepath
+def import_golab_tevc(filepath: str = '', parent: QWidget = None) -> tuple[xr.Dataset, str]:
+    if filepath == '':
+        filepath, _filter = QFileDialog.getOpenFileName(parent, 'Import GoLab TEVC', '', 'GoLab TEVC (*.mat)')
+        if filepath == '':
+            return None
+    matdict = sp.io.loadmat(filepath, simplify_cells=True)
+    # print(matdict)
+    current = matdict['current']
+    current_units = matdict['current_units']
+    if len(current_units) > 1:
+        prefix = current_units[0]
+        if prefix in metric_scale_factors:
+            current *= metric_scale_factors[prefix]
+            current_units = current_units[1:]
+    time = np.arange(len(current)) * matdict['time_interval_sec']
+    ds = xr.Dataset(
+        data_vars={
+            'current': (['time'], current, {'units': current_units}),
+        },
+        coords={
+            'time': (['time'], time, {'units': 's'}),
+        },
+    )
+    if 'events' in matdict and matdict['events']:
+        ds.attrs['regions'] = []
+        for event in matdict['events']:
+            time = event['time_sec']
+            text = event['text']
+            ds.attrs['regions'].append({
+                'region': {'time': [time, time]},
+                'text': text,
+            })
+    if 'notes' in matdict:
+        ds.attrs['notes'] = matdict['notes']
+    return ds, filepath
 
 
 def test_live():