Added "Line cross section" feature

Author: PierreRaybaut

doc/features/panels/overview.rst

@@ -25,3 +25,4 @@ The built-in panels are:
 * :py:data:`plotpy.constants.ID_XCS`: `X-axis cross section` panel
 * :py:data:`plotpy.constants.ID_YCS`: `Y-axis cross section` panel
 * :py:data:`plotpy.constants.ID_OCS`: `oblique cross section` panel
+* :py:data:`plotpy.constants.ID_LCS`: `line cross section` panel

doc/features/tools/overview.rst

@@ -64,6 +64,7 @@ The `tools` module provides the following tools:
 * :py:class:`.tools.YCSPanelTool`
 * :py:class:`.tools.CrossSectionTool`
 * :py:class:`.tools.AverageCrossSectionTool`
+* :py:class:`.tools.LineCrossSectionTool`
 * :py:class:`.tools.SaveAsTool`
 * :py:class:`.tools.CopyToClipboardTool`
 * :py:class:`.tools.OpenFileTool`

doc/features/tools/reference.rst

@@ -77,6 +77,8 @@ Reference
    :members:
 .. autoclass:: plotpy.tools.AverageCrossSectionTool
    :members:
+.. autoclass:: plotpy.tools.LineCrossSectionTool
+   :members:
 .. autoclass:: plotpy.tools.SaveAsTool
    :members:
 .. autoclass:: plotpy.tools.CopyToClipboardTool

plotpy/constants.py

@@ -71,6 +71,8 @@ class PlotType(enum.Enum):
 ID_YCS = "y_cross_section"
 #: ID of the `oblique averaged cross section` panel
 ID_OCS = "oblique_cross_section"
+#: ID of the `line cross section` panel
+ID_LCS = "line_cross_section"
 
 
 # ===============================================================================

plotpy/images/csection_line.png

@@ -16,6 +16,7 @@ class from which all panels must derived from) and identifiers for each kind
 .. autodata:: plotpy.constants.ID_XCS
 .. autodata:: plotpy.constants.ID_YCS
 .. autodata:: plotpy.constants.ID_OCS
+.. autodata:: plotpy.constants.ID_LCS
 
 .. autoclass:: PanelWidget
     :members:

plotpy/panels/base.py

@@ -1,6 +1,10 @@
 # -*- coding: utf-8 -*-
+
+from __future__ import annotations
+
 import sys
 import weakref
+from typing import TYPE_CHECKING
 
 import numpy as np
 from qtpy import QtCore as QC
@@ -12,6 +16,9 @@
 from plotpy.items.image.misc import get_image_from_qrect
 from plotpy.mathutils.geometry import rotate, translate, vector_angle, vector_norm
 
+if TYPE_CHECKING:
+    from plotpy.items import AnnotatedObliqueRectangle, AnnotatedSegment
+
 try:
     from plotpy._scaler import INTERP_LINEAR, _scale_tr
 except ImportError:
@@ -434,14 +441,8 @@ class ObliqueCrossSectionItem(CrossSectionItem):
 
     DEBUG = False
 
-    def __init__(self, curveparam=None, errorbarparam=None):
-        CrossSectionItem.__init__(self, curveparam, errorbarparam)
-
-    def update_curve_data(self, obj):
-        """
-
-        :param obj:
-        """
+    def update_curve_data(self, obj: AnnotatedObliqueRectangle) -> None:
+        """Update curve data"""
         source = self.get_source_image()
         rect = obj.get_bounding_rect_coords()
         if rect is not None and source.data is not None:
@@ -455,3 +456,51 @@ def update_curve_data(self, obj):
     def update_scale(self):
         """ """
         pass
+
+
+def compute_line_section(
+    data: np.ndarray, row0, col0, row1, col1
+) -> tuple[np.ndarray, np.ndarray]:
+    """Return intensity profile of data along a line
+
+    Args:
+        data: 2D array
+        row0, col0: start point
+        row1, col1: end point
+    """
+    # Keep coordinates inside the image
+    row0 = max(0, min(row0, data.shape[0] - 1))
+    col0 = max(0, min(col0, data.shape[1] - 1))
+    row1 = max(0, min(row1, data.shape[0] - 1))
+    col1 = max(0, min(col1, data.shape[1] - 1))
+    # Keep coordinates in the right order
+    row0, row1 = min(row0, row1), max(row0, row1)
+    col0, col1 = min(col0, col1), max(col0, col1)
+    # Extract the line
+    line = np.zeros((2, max(abs(row1 - row0), abs(col1 - col0)) + 1), dtype=np.float64)
+    line[0, :] = np.linspace(row0, row1, line.shape[1])
+    line[1, :] = np.linspace(col0, col1, line.shape[1])
+    # Interpolate the line
+    return line[1, :], np.array([data[int(r), int(c)] for r, c in line.T])
+
+
+# Line cross section item
+class LineCrossSectionItem(CrossSectionItem):
+    """A Qwt item representing line cross section data"""
+
+    def update_curve_data(self, obj: AnnotatedSegment) -> None:
+        """Update curve data"""
+        source = self.get_source_image()
+        rect = obj.get_rect()
+        if rect is not None and source.data is not None:
+            x0, y0, x1, y1 = obj.get_rect()
+            c0, r0 = source.get_closest_pixel_indexes(x0, y0)
+            c1, r1 = source.get_closest_pixel_indexes(x1, y1)
+            sectx, secty = compute_line_section(source.data, r0, c0, r1, c1)
+            if secty.size == 0 or np.all(np.isnan(secty)):
+                sectx, secty = np.array([]), np.array([])
+            self.process_curve_data(sectx, secty, None, None)
+
+    def update_scale(self):
+        """ """
+        pass

plotpy/panels/csection/csitem.py

@@ -12,6 +12,7 @@
 from plotpy.constants import LUT_MAX, PlotType
 from plotpy.interfaces import ICSImageItemType
 from plotpy.panels.csection.csitem import (
+    LineCrossSectionItem,
     ObliqueCrossSectionItem,
     XCrossSectionItem,
     YCrossSectionItem,
@@ -430,6 +431,7 @@ class ObliqueCrossSectionPlot(HorizontalCrossSectionPlot):
     PLOT_TITLE = _("Oblique averaged cross section")
     CURVE_LABEL = _("Oblique averaged cross section")
     LABEL_TEXT = _("Activate the oblique cross section tool")
+    SHADE = 0.0
 
     def __init__(self, parent=None):
         super().__init__(parent)
@@ -446,3 +448,26 @@ def create_cross_section_item(self):
     def axis_dir_changed(self, plot, axis_id):
         """An axis direction has changed"""
         pass
+
+
+# Line cross section plot
+class LineCrossSectionPlot(HorizontalCrossSectionPlot):
+    """Line cross section plot"""
+
+    PLOT_TITLE = _("Line cross section")
+    CURVE_LABEL = _("Line cross section")
+    LABEL_TEXT = _("Activate the line cross section tool")
+    SHADE = 0.0
+
+    def __init__(self, parent=None):
+        super().__init__(parent)
+        self.set_title(self.PLOT_TITLE)
+        self.single_source = True
+
+    def create_cross_section_item(self) -> LineCrossSectionItem:
+        """Create cross section item"""
+        return LineCrossSectionItem(self.param)
+
+    def axis_dir_changed(self, plot, axis_id):
+        """An axis direction has changed"""
+        pass

plotpy/panels/csection/csplot.py

@@ -7,11 +7,12 @@
 from qtpy import QtWidgets as QW
 
 from plotpy.config import _
-from plotpy.constants import ID_OCS, ID_XCS, ID_YCS
+from plotpy.constants import ID_LCS, ID_OCS, ID_XCS, ID_YCS
 from plotpy.interfaces import IPanel
 from plotpy.panels.base import PanelWidget
 from plotpy.panels.csection.csplot import (
     CrossSectionPlot,
+    LineCrossSectionPlot,
     ObliqueCrossSectionPlot,
     XCrossSectionPlot,
     YCrossSectionPlot,
@@ -397,3 +398,18 @@ def setup_actions(self):
         super().setup_actions()
         self.lockscales_ac.setChecked(False)
         self.autoscale_ac.setChecked(True)
+
+
+class LineCrossSection(CrossSectionWidget):
+    """Line cross section panel
+
+    Args:
+        parent: parent widget
+    """
+
+    PANEL_ID = ID_LCS
+    CrossSectionPlotKlass = LineCrossSectionPlot
+
+    def __init__(self, parent=None):
+        super().__init__(parent)
+        self.cs_plot.set_axis_direction("bottom", reverse=False)

plotpy/panels/csection/cswidget.py

@@ -0,0 +1,80 @@
+# -*- coding: utf-8 -*-
+#
+# Licensed under the terms of the BSD 3-Clause
+# (see plotpy/LICENSE for details)
+
+"""Line cross section test"""
+
+# guitest: show
+
+from guidata.qthelpers import qt_app_context
+
+from plotpy.builder import make
+from plotpy.panels.csection.cswidget import LineCrossSection
+from plotpy.plot import PlotDialog, PlotOptions
+from plotpy.tests import get_path
+from plotpy.tools import ImageMaskTool, LCSPanelTool, LineCrossSectionTool
+
+
+class BaseCSImageDialog(PlotDialog):
+    """Base cross section test
+
+    This class is used to test the LineCrossSection and ObliqueCrossSection
+    """
+
+    TOOLCLASSES = ()
+    PANELCLASS = None
+
+    def __init__(self, parent=None, toolbar=True, title=None, options=None):
+        super().__init__(
+            parent=parent,
+            toolbar=toolbar,
+            title=title,
+            options=options,
+            auto_tools=True,
+        )
+        for tool in self.TOOLCLASSES:
+            self.manager.add_tool(tool)
+
+    def populate_plot_layout(self):
+        """Populate the plot layout"""
+        super().populate_plot_layout()
+        cs_panel = self.PANELCLASS(self)
+        splitter = self.plot_widget.xcsw_splitter
+        splitter.addWidget(cs_panel)
+        splitter.setSizes([0, 1, 0])
+        self.manager.add_panel(cs_panel)
+
+
+class LCSImageDialog(BaseCSImageDialog):
+    """Line cross section test"""
+
+    TOOLCLASSES = (LineCrossSectionTool, LCSPanelTool, ImageMaskTool)
+    PANELCLASS = LineCrossSection
+
+
+def generic_cross_section_dialog(title, dialogclass):
+    """Generic function used to test the cross section tools"""
+    with qt_app_context(exec_loop=True):
+        win = dialogclass(
+            toolbar=True,
+            title=title,
+            options=PlotOptions(type="image"),
+        )
+        win.resize(600, 600)
+        filename = get_path("brain_cylinder.png")
+        image = make.maskedimage(filename=filename, colormap="bone")
+        plot = win.manager.get_plot()
+        plot.add_item(image)
+        plot.set_active_item(image)
+        image.unselect()
+        win.show()
+
+
+def test_cross_section_line():
+    """Test cross section oblique"""
+    generic_cross_section_dialog("Line cross section test", LCSImageDialog)
+
+
+if __name__ == "__main__":
+    test_cross_section_line()