xarray-graph 0.2.0__tar.gz → 0.2.2__tar.gz

{xarray_graph-0.2.0 → xarray_graph-0.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: xarray-graph
-Version: 0.2.0
+Version: 0.2.2
 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
@@ -20,11 +20,11 @@ Project-URL: Repository, https://github.com/marcel-goldschen-ohm/xarray-graph
 Requires-Python: >=3.9
 Requires-Dist: numpy>=1.26.2
 Requires-Dist: xarray>=2023.12.0
-Requires-Dist: xarray-tree>=0.1.0
 Requires-Dist: qtpy>=2.4.1
 Requires-Dist: qtawesome>=1.3.0
-Requires-Dist: pyqt-ext>=1.1.0
-Requires-Dist: pyqtgraph-ext>=1.0.0
+Requires-Dist: pyqt-ext>=1.2.1
+Requires-Dist: pyqtgraph-ext>=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
@@ -38,6 +38,11 @@ Should work with PySide6, PyQt6, or PyQt5.
 pip install PySide6 xarray-graph
 ```
 
+# Run
+```shell
+xarray-graph
+```
+
 # TODO
 - i/o
 - tests

{xarray_graph-0.2.0 → xarray_graph-0.2.2}/README.md

@@ -7,6 +7,11 @@ Should work with PySide6, PyQt6, or PyQt5.
 pip install PySide6 xarray-graph
 ```
 
+# Run
+```shell
+xarray-graph
+```
+
 # TODO
 - i/o
 - tests

{xarray_graph-0.2.0 → xarray_graph-0.2.2}/pyproject.toml

@@ -9,11 +9,11 @@ requires-python = ">=3.9"
 dependencies = [
     "numpy>=1.26.2",
     "xarray>=2023.12.0",
-    "xarray-tree>=0.1.0",
     "qtpy>=2.4.1",
     "qtawesome>=1.3.0",
-    "pyqt-ext>=1.1.0",
-    "pyqtgraph-ext>=1.0.0",
+    "pyqt-ext>=1.2.1",
+    "pyqtgraph-ext>=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 = "0.2.0"
+version = "0.2.2"
 
 [project.license]
 text = "MIT"
@@ -45,7 +45,7 @@ homepage = "https://github.com/marcel-goldschen-ohm/xarray-graph"
 repository = "https://github.com/marcel-goldschen-ohm/xarray-graph"
 
 [project.scripts]
-xrg = "xarray_graph.__main__:main"
+xarray-graph = "xarray_graph.__main__:main"
 
 [build-system]
 requires = [

{xarray_graph-0.2.0 → xarray_graph-0.2.2}/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])
     
@@ -1034,6 +1024,17 @@ class XarrayGraph(QMainWindow):
             if i != index:
                 button.setChecked(False)
     
+    def _show_control_panel_at(self, index: int) -> None:
+        actions = self._control_panel_toolbar.actions()
+        widgets = [self._control_panel_toolbar.widgetForAction(action) for action in actions]
+        buttons = [widget for widget in widgets if isinstance(widget, QToolButton)]
+        buttons[index].setChecked(True)
+        self._control_panel.setCurrentIndex(index)
+        self._control_panel.setVisible(True)
+        for i, button in enumerate(buttons):
+            if i != index:
+                button.setChecked(False)
+    
     def _setup_data_control_panel(self) -> None:
         button = QToolButton()
         button.setIcon(qta.icon('ph.eye', options=[{'opacity': 0.5}]))
@@ -1043,7 +1044,8 @@ 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)
@@ -1051,6 +1053,7 @@ 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)
@@ -1060,7 +1063,7 @@ 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)
@@ -2196,43 +2199,41 @@ 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():

xarray_graph-0.2.2/src/xarray_graph/__main__.py

@@ -0,0 +1,76 @@
+from xarray_graph.XarrayGraph import XarrayGraph
+from qtpy.QtCore import QTimer
+from qtpy.QtWidgets import QApplication
+
+
+def main():
+    app = QApplication()
+    ui = XarrayGraph()
+    # ui.setWindowTitle(ui.__class__.__name__)
+    ui.setWindowTitle('xarray-graph')
+    ui.show()
+    QTimer.singleShot(100, lambda: ask_for_example(ui))
+    app.exec()
+
+
+def ask_for_example(ui: XarrayGraph):
+    from qtpy.QtWidgets import QMessageBox
+
+    example = QMessageBox.question(ui, 'Example?', 'Load example data?')
+    if example == QMessageBox.StandardButton.Yes:
+        load_example(ui)
+
+
+def load_example(ui: XarrayGraph):
+    import numpy as np
+    import xarray as xr
+    from datatree import DataTree
+
+    n = 100
+    raw_ds = xr.Dataset(
+        data_vars={
+            'current': (['series', 'sweep', 'time'], np.random.rand(3, 10, n) * 1e-9, {'units': 'A'}),
+            'voltage': (['series', 'sweep', 'time'], np.random.rand(3, 10, n) * 10000, {'units': 'V'}),
+        },
+        coords={
+            'series': ('series', np.arange(3)),
+            'sweep': ('sweep', np.arange(10)),
+            'time': ('time', np.arange(n) * 0.01, {'units': 's'}),
+        },
+    )
+
+    baselined_ds = xr.Dataset(
+        data_vars={
+            'current': (['series', 'sweep', 'time'], np.random.rand(3, 10, n) * 1e-9, {'units': 'A'}),
+        },
+        coords={
+            'series': ('series', np.arange(3)),
+            'sweep': ('sweep', np.arange(10)),
+            'time': ('time', np.arange(n) * 0.01, {'units': 's'}),
+        },
+    )
+
+    scaled_ds = xr.Dataset(
+        data_vars={
+            'current': (['series', 'sweep', 'time'], np.random.rand(1, 2, n) * 1e-9, {'units': 'A'}),
+        },
+        coords={
+            'series': ('series', [1]),
+            'sweep': ('sweep', [5,8]),
+            'time': ('time', np.arange(n) * 0.01, {'units': 's'}),
+        },
+    )
+    
+    root_node = DataTree()
+    raw_node = DataTree(name='raw', data=raw_ds, parent=root_node)
+    baselined_node = DataTree(name='baselined', data=baselined_ds, parent=raw_node)
+    scaled_node = DataTree(name='scaled', data=scaled_ds, parent=baselined_node)
+
+    ui.data = root_node
+
+    ui._show_control_panel_at(0)
+    ui._data_treeview.expandAll()
+
+
+if __name__ == '__main__':
+    main()

xarray_graph-0.2.0/src/xarray_graph/__main__.py

@@ -1,14 +0,0 @@
-from xarray_graph.XarrayGraph import XarrayGraph
-from qtpy.QtWidgets import QApplication
-
-
-def main():
-    app = QApplication()
-    ui = XarrayGraph()
-    ui.setWindowTitle(ui.__class__.__name__)
-    ui.show()
-    app.exec()
-
-
-if __name__ == '__main__':
-    main()