v0.3.1 release

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "pickmix"
-version = "0.3.0"
+version = "0.3.1"
 description = "Multi-kind particle picking GUI for cryo-ET sub-tomogram averaging workflows."
 readme = "README.md"
 authors = [

src/pickmix/gui/dialogs/kind_dialog.py

@@ -33,7 +33,7 @@ class KindDialog(QDialog):
     # __init__: build the form; name and kind are None when adding, others are the kinds besides this one (so the parent choices and the names this kind cannot take), and check returns why a name and kind cannot be saved, or None
     def __init__(
         self, parent: QWidget | None, name: str | None, kind: Kind | None, others: list[str],
-        check: Callable[[str, Kind], str | None],
+        check: Callable[[str, Kind], str | None], *, tomo_angpix: float | None = None,
     ) -> None:
         super().__init__(parent)
         self._check = check
@@ -61,7 +61,12 @@ def __init__(
         self.tilt_box.setChecked(kind.tilt_prior_deg is not None)
         self.tilt_spin.setEnabled(self.tilt_box.isChecked())
         self.tilt_box.toggled.connect(self.tilt_spin.setEnabled)
-        self.angpix_spin = _spin(kind.extract_angpix, minimum=0.01)
+        self.angpix_spin = _spin(kind.extract_angpix, minimum=0.01, decimals=3)
+        self.tomo_button = QPushButton('Tomogram')
+        self.tomo_button.setVisible(tomo_angpix is not None)
+        if tomo_angpix is not None:
+            self.tomo_button.setToolTip(f'Use the tomogram pixel size, {tomo_angpix:g} Å/px')
+            self.tomo_button.clicked.connect(lambda: self.angpix_spin.setValue(tomo_angpix))
         self.error = QLabel()
         error_look(self.error)
         self.error.setWordWrap(True)
@@ -74,6 +79,9 @@ def __init__(
         colour_row = QHBoxLayout()
         colour_row.addWidget(self.colour_edit)
         colour_row.addWidget(choose)
+        angpix_row = QHBoxLayout()
+        angpix_row.addWidget(self.angpix_spin, 1)
+        angpix_row.addWidget(self.tomo_button)        
         tilt_row = QHBoxLayout()
         tilt_row.addWidget(self.tilt_box)
         tilt_row.addWidget(self.tilt_spin)
@@ -88,7 +96,7 @@ def __init__(
         layout.addWidget(self._section('Estimation', [
             ('estimator', self.estimator_box), ('parent', self.parent_box), ('parent_tolerance_a', self.tolerance_spin),
         ]))
-        layout.addWidget(self._section('Extraction', [('tilt_prior_deg', tilt_row), ('extract_angpix', self.angpix_spin)]))
+        layout.addWidget(self._section('Extraction', [('tilt_prior_deg', tilt_row), ('extract_angpix', angpix_row)]))
         layout.addWidget(self.error)
         layout.addLayout(footer)
 
@@ -142,10 +150,10 @@ def _choose_colour(self) -> None:
         if colour.isValid():
             self.colour_edit.setText(colour.name())
 
-# _spin: a float spin box with two decimals
-def _spin(value: float, *, minimum: float = 0.0, maximum: float = 1_000_000.0) -> QDoubleSpinBox:
+# _spin: a float spin box, two decimals unless asked for more
+def _spin(value: float, *, minimum: float = 0.0, maximum: float = 1_000_000.0, decimals: int = 2) -> QDoubleSpinBox:
     box = QDoubleSpinBox()
     box.setRange(minimum, maximum)
-    box.setDecimals(2)
+    box.setDecimals(decimals)
     box.setValue(value)
     return box

src/pickmix/gui/panes/kinds_pane.py

@@ -147,7 +147,7 @@ def _edit(self, name: str | None) -> None:
         if self.project is None:
             return
         kinds = self.project.config.kinds
-        dialog = KindDialog(self, name, None if name is None else kinds[name], [k for k in kinds if k != name], lambda new, kind: self._problem(new, kind, name))
+        dialog = KindDialog(self, name, None if name is None else kinds[name], [k for k in kinds if k != name], lambda new, kind: self._problem(new, kind, name), tomo_angpix=self.project.common_pixel_size)
         result = dialog.exec()
         if result == DELETED and name is not None:
             self._delete(name)

src/pickmix/project.py

@@ -3,6 +3,7 @@
 '''
 
 # Import external dependencies
+from collections import Counter
 from collections.abc import Sequence
 from dataclasses import dataclass
 from pathlib import Path
@@ -27,6 +28,12 @@ def update(self, **changes: object) -> None:
         save_config(config, self.path)
         self.config = config
 
+    # common_pixel_size: pixel size most tomograms share in A/px
+    @property
+    def common_pixel_size(self) -> float | None:
+        sizes = Counter(round(t.pixel_size, 3) for t in self.tomos.values())
+        return sizes.most_common(1)[0][0] if sizes else None
+
     # display_name: the configured name, else the name of the directory holding config.toml
     @property
     def display_name(self) -> str:

tests/gui/test_dialogs.py

@@ -34,6 +34,17 @@ def test_defaults_when_adding(self, qtbot: QtBot) -> None:
         dialog.name_edit.setText('yellow')
         assert dialog.values() == ('yellow', Kind(marker_a=100, box_a=100))
 
+    # test_tomogram_pixel_size_button: button fills the extract pixel size with tomogram's, and only shows when it is known
+    def test_tomogram_pixel_size_button(self, qtbot: QtBot) -> None:
+        dialog = KindDialog(None, 'cage', Kind(marker_a=600), [], _ok, tomo_angpix=5.36)
+        qtbot.addWidget(dialog)
+        assert not dialog.tomo_button.isHidden() and dialog.values()[1].extract_angpix == 10.68
+        dialog.tomo_button.click()
+        assert dialog.values()[1].extract_angpix == 5.36
+        plain = KindDialog(None, 'cage', Kind(marker_a=600), [], _ok)
+        qtbot.addWidget(plain)
+        assert plain.tomo_button.isHidden()
+
     # test_delete_only_when_editing: an existing kind can be deleted, a new one cannot
     def test_delete_only_when_editing(self, qtbot: QtBot) -> None:
         dialog = KindDialog(None, 'cage', Kind(marker_a=600), [], _ok)

tests/test_project.py

@@ -60,3 +60,10 @@ def test_create_with_name(self, tmp_path: Path, relion_project: Callable[[Path,
         (tmp_path / 'raw').mkdir()
         path, _ = create_project(tmp_path / 'proj', [('r1', tmp_path / 'p')], 'Tomograms/job006', tmp_path / 'raw', name='Cages')
         assert load_config(path).name == 'Cages'
+
+    # test_common_pixel_size: the pixel size most tomograms share, None when there are none
+    def test_common_pixel_size(self, make_config: Callable[..., Path]) -> None:
+        project = open_project(make_config())
+        assert project.common_pixel_size == 5.36
+        project.tomos = {}
+        assert project.common_pixel_size is None