phaseplot widget, export layers to yt ds

docs/examples/PhasePlotTempExample.ipynb

@@ -0,0 +1,105 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "631b90ba-e543-4078-b234-4fc7b18c8fbf",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "[<Image layer 'nuclei' at 0x76b12a76d0f0>,\n",
+       " <Image layer 'WGA' at 0x76b12a217c70>,\n",
+       " <Image layer 'actin' at 0x76b12a28a9e0>]"
+      ]
+     },
+     "execution_count": 1,
+     "metadata": {},
+     "output_type": "execute_result"
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "yt : [INFO     ] 2024-11-21 14:42:35,829 Parameters: current_time              = 0.0\n",
+      "yt : [INFO     ] 2024-11-21 14:42:35,830 Parameters: domain_dimensions         = [ 16 512 512]\n",
+      "yt : [INFO     ] 2024-11-21 14:42:35,831 Parameters: domain_left_edge          = [0. 0. 0.]\n",
+      "yt : [INFO     ] 2024-11-21 14:42:35,832 Parameters: domain_right_edge         = [1. 1. 1.]\n",
+      "yt : [INFO     ] 2024-11-21 14:42:35,832 Parameters: cosmological_simulation   = 0\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "x\n",
+      "y\n",
+      "nuclei\n",
+      "nuclei\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "yt : [INFO     ] 2024-11-21 14:43:09,699 Parameters: current_time              = 0.0\n",
+      "yt : [INFO     ] 2024-11-21 14:43:09,700 Parameters: domain_dimensions         = [ 16 512 512]\n",
+      "yt : [INFO     ] 2024-11-21 14:43:09,700 Parameters: domain_left_edge          = [0. 0. 0.]\n",
+      "yt : [INFO     ] 2024-11-21 14:43:09,701 Parameters: domain_right_edge         = [1. 1. 1.]\n",
+      "yt : [INFO     ] 2024-11-21 14:43:09,702 Parameters: cosmological_simulation   = 0\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "nuclei\n",
+      "WGA\n",
+      "actin\n",
+      "x\n"
+     ]
+    }
+   ],
+   "source": [
+    "import napari \n",
+    "import yt \n",
+    "\n",
+    "v = napari.Viewer()\n",
+    "v.open_sample(\n",
+    "    plugin = 'napari', \n",
+    "    sample = 'kidney',\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2e92b80f-7ee3-4e72-9dd7-aff1a0342689",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

pyproject.toml

@@ -12,3 +12,8 @@ validate_release = { cmd = "python repo_utilities/validate.py", help = "validate
 update_schema_docs = { cmd = "python repo_utilities/update_schema_docs.py", help = "updates the schema related documentation" }
 update_sample_data = { cmd = "python repo_utilities/update_sample_data.py", help = "updates sample data code" }
 test = "pytest -v --color=yes --cov=yt_napari --cov-report=html"
+
+[tool.pytest.ini_options]
+filterwarnings = [
+    'ignore:\s*Pyarrow will become a required dependency of pandas:DeprecationWarning',
+]

setup.cfg

@@ -39,6 +39,7 @@ install_requires =
     qtpy
     unyt
     yt>=4.0.1
+    superqt
 python_requires = >=3.10
 package_dir =
     =src

src/yt_napari/_gui_utilities.py

@@ -4,6 +4,7 @@
 import pydantic
 from magicgui import type_map, widgets
 from pydantic_core import PydanticUndefinedType
+from qtpy.QtWidgets import QLayout
 
 from yt_napari import _data_model
 from yt_napari.logging import ytnapari_log
@@ -380,3 +381,11 @@ def get_yt_metadata_container():
 def _is_base_model_or_yt_obj(field_info: pydantic.fields.FieldInfo):
     ftype = field_info.annotation
     return ftype in _data_model._data_model_list
+
+
+def clearLayout(layout: QLayout):
+    # remove all widgets from a layout
+    while layout.count():
+        child = layout.takeAt(0)
+        if child.widget():
+            child.widget().deleteLater()

src/yt_napari/_tests/test_layers_to_yt.py

@@ -0,0 +1,81 @@
+import napari
+import numpy as np
+import pytest
+from yt.data_objects.static_output import Dataset
+
+from yt_napari.viewer import layers_to_yt
+
+
+@pytest.fixture
+def some_images():
+
+    sh = (8, 16, 32)
+    n_images = 4
+    images = []
+
+    for im in range(n_images):
+        images.append(
+            {
+                "value": np.random.random(sh),
+                "name": f"image_{im}",
+            }
+        )
+
+    return images
+
+
+def test_layers_to_yt(
+    make_napari_viewer,
+    some_images,
+):
+
+    viewer: napari.Viewer = make_napari_viewer()
+
+    for im in some_images:
+        viewer.add_image(im["value"], name=im["name"])
+
+    bbox = np.array([[-1.0, 1.0], [-1.0, 1.0], [-1.5, 2.0]])
+    ds = layers_to_yt(viewer, layers=["image_0", "image_1"], bbox=bbox)
+
+    assert isinstance(ds, Dataset)
+    assert len(ds.field_list) == 2
+
+
+def test_layers_bad_names(make_napari_viewer, some_images):
+    viewer: napari.Viewer = make_napari_viewer()
+    for im in some_images:
+        viewer.add_image(im["value"], name=im["name"])
+
+    with pytest.raises(RuntimeError, match="Layer notalayer not found"):
+        _ = layers_to_yt(viewer, layers=["image_0", "notalayer"])
+
+    with pytest.raises(RuntimeError, match="Layer 100 not found"):
+        _ = layers_to_yt(viewer, layers=[0, 100])
+
+
+def test_layers_bad_shape(make_napari_viewer, some_images):
+    viewer: napari.Viewer = make_napari_viewer()
+    for im in some_images:
+        viewer.add_image(im["value"], name=im["name"])
+
+    viewer.add_image(np.random.random((10, 10, 20)), name="bad_shape")
+
+    with pytest.raises(RuntimeError, match="Layer notalayer not found"):
+        _ = layers_to_yt(viewer, layers=["image_0", "notalayer"])
+
+    with pytest.raises(RuntimeError, match="Can only export layers as a yt dataset"):
+        _ = layers_to_yt(viewer)
+
+
+def test_additional_kwargs(
+    make_napari_viewer,
+    some_images,
+):
+    viewer: napari.Viewer = make_napari_viewer()
+
+    for im in some_images:
+        viewer.add_image(im["value"], name=im["name"])
+
+    ds = layers_to_yt(viewer, length_unit="km")
+    assert len(ds.field_list) == len(some_images)
+    assert ds.domain_right_edge.to("km")[2].d == 1

src/yt_napari/_tests/test_phaseplot_widget.py

@@ -0,0 +1,170 @@
+import os
+
+import numpy as np
+import pytest
+from napari import Viewer
+from qtpy.QtWidgets import QComboBox, QVBoxLayout
+from yt.visualization.profile_plotter import PhasePlot
+
+from yt_napari._widget_2d_plots import YTPhasePlot, _validate_cmyt_name
+
+
+@pytest.fixture
+def some_images():
+
+    sh = (8, 16, 32)
+    n_images = 3
+    images = []
+
+    for im in range(n_images):
+        images.append(
+            {
+                "value": np.random.random(sh),
+                "name": f"image_{im}",
+            }
+        )
+
+    return images
+
+
+def test_phaseplot_widget(
+    make_napari_viewer,
+    some_images,
+    tmp_path,
+):
+
+    viewer: Viewer = make_napari_viewer()
+    r = YTPhasePlot(napari_viewer=viewer)
+
+    for im in some_images:
+        viewer.add_image(im["value"], name=im["name"])
+
+    # check that layers are populated
+    r.update_layers.native.click()
+    for layer in viewer.layers:
+        assert layer.name in r.available_layer_list
+
+    r.render_button.native.click()
+    assert isinstance(r.phase_plot, PhasePlot)
+
+    r.callback_container.apply_logx.value = True
+    r.callback_container.apply_logy.value = True
+    r.callback_container.apply_logz.value = True
+    r.callback_container.reverse_cmap.value = True
+    r.callback_container.save.value = True
+
+    svfig = str(tmp_path / "pp_fig.png")
+    r.callback_container.savename.value = svfig
+    r.run_callback_button.native.click()
+    assert os.path.isfile(svfig)
+
+    r.deleteLater()
+
+
+def test_phaseplot_fields(
+    make_napari_viewer,
+    some_images,
+):
+    viewer: Viewer = make_napari_viewer()
+    r = YTPhasePlot(napari_viewer=viewer)
+
+    for im in some_images:
+        viewer.add_image(im["value"], name=im["name"])
+
+    r.update_layers.native.click()
+
+    r.layer_1.setCurrentIndex(len(some_images))
+    assert r.layer_1.currentText() == r._default_index_fields[0]
+    assert r.layer_1.currentIndex() == len(some_images)
+
+    r.render_button.native.click()
+
+    r.deleteLater()
+
+
+def test_weight_field(
+    make_napari_viewer,
+    some_images,
+):
+    viewer: Viewer = make_napari_viewer()
+    r = YTPhasePlot(napari_viewer=viewer)
+
+    for im in some_images:
+        viewer.add_image(im["value"], name=im["name"])
+
+    r.update_layers.native.click()
+
+    r.layer_4_weight.setCurrentIndex(1)
+    assert r.layer_4_weight.currentText() == some_images[0]["name"]
+
+    r.render_button.native.click()
+    r.deleteLater()
+
+
+def test_apply_callbacks_without_render(
+    make_napari_viewer,
+    some_images,
+):
+    viewer: Viewer = make_napari_viewer()
+    r = YTPhasePlot(napari_viewer=viewer)
+
+    for im in some_images:
+        viewer.add_image(im["value"], name=im["name"])
+
+    r.update_layers.native.click()
+
+    assert r.phase_plot is None
+    r.run_callback_button.native.click()
+    assert isinstance(r.phase_plot, PhasePlot)
+    r.deleteLater()
+
+
+@pytest.mark.parametrize(
+    "input_name,expected",
+    [("cmapname.cmyt", "cmyt.cmapname"), ("notacmytcmap", "notacmytcmap")],
+)
+def test_validate_cmyt_name(input_name: str, expected: str):
+    result = _validate_cmyt_name(input_name)
+    assert result == expected
+
+
+def test_add_layer_dropdown(
+    make_napari_viewer,
+    some_images,
+):
+    viewer: Viewer = make_napari_viewer()
+    r = YTPhasePlot(napari_viewer=viewer)
+
+    for im in some_images:
+        viewer.add_image(im["value"], name=im["name"])
+
+    r.update_layers.native.click()
+
+    sub_QVbox = QVBoxLayout()
+
+    r.add_layer_dropdown(
+        "teststr",
+        "teststr2",
+        sub_QVbox,
+        value=None,
+    )
+    n_items = sub_QVbox.count()
+    index = n_items - 1
+    # dropdown gets added to an inner layout
+    layer_hbox = sub_QVbox.itemAt(index).layout()
+    # should be 2 widgets here
+    n_items = layer_hbox.count()
+    assert n_items == 2
+    assert isinstance(layer_hbox.itemAt(1).widget(), QComboBox)
+
+    r.add_layer_dropdown(
+        "teststr",
+        "teststr2",
+        sub_QVbox,
+        value=None,
+        value_index=100,
+    )
+
+    sub_QVbox.deleteLater()
+
+    r.deleteLater()