Merge pull request #67 from PlotPyStack/develop

Develop v2.10.0

Author: ThomasMalletCodra

doc/release_notes/release_2.10.md

@@ -0,0 +1,34 @@
+# Version 2.10 #
+
+## PlotPy Version 2.10.0 ##
+
+✨ New features:
+
+* **Per-axis autoscale strategy**: Added configurable autoscale behavior for each axis via the axis parameters dialog. Three strategies are available: *Auto* (default — compute bounds from items), *Fixed range* (apply user-defined Min/Max values) and *Disabled* (leave the axis untouched on autoscale). New API: `BasePlot.set_axis_autoscale_strategy()` / `BasePlot.get_axis_autoscale_strategy()` (closes [Issue #63](https://github.com/PlotPyStack/PlotPy/issues/63), partial)
+* **Symbol border width**: Added an `edgewidth` parameter to `SymbolParam` for customizable marker border thickness — previously the border was always 1 pixel wide
+
+🛠️ Bug fixes:
+
+* **Rectangular snapshot tool** — Fixed the "Original size" computation (closes [Issue #57](https://github.com/PlotPyStack/PlotPy/issues/57)):
+  * The preview no longer displays negative dimensions when the X or Y axis is
+    reversed
+  * The "Original size" is now computed from pixel coordinates instead of axis
+    units, so it is correct for `XYImageItem` (and any item with non-uniform
+    axis scaling) regardless of axis orientation
+  * The `ValueError` raised by the resize dialog when the selection produced
+    negative dimensions on a reversed axis is gone
+  * Selecting a region larger than the plotted image now reports the same
+    native pixel resolution for both `ImageItem` and `XYImageItem`
+    (previously `XYImageItem` reported ``shape - 1`` while `ImageItem`
+    reported the full oversized resolution): exporting at "Original size"
+    now consistently preserves the source pixel density and avoids
+    upsampling, regardless of the item type
+* **Snapshot tool cursor** — Fixed the mouse cursor remaining stuck as a cross (`+`) outside the plot canvas (axes, toolbar) after using the snapshot tool. The modal dialogs are now opened after Qt has released the implicit pointer grab, so the cursor is correctly restored (closes [Issue #58](https://github.com/PlotPyStack/PlotPy/issues/58))
+* **Z-axis log tool** — Fixed the `ZAxisLogTool` being always disabled for non-`ImageItem` image types (`XYImageItem`, `MaskedImageItem`, `MaskedXYImageItem`, `TrImageItem`, `RGBImageItem`). The Z-axis log API (`get_zaxis_log_state` / `set_zaxis_log_state`) was moved from `ImageItem` up to `BaseImageItem` so all image item types support it. This notably fixes the tool being permanently greyed out in DataLab's image panel (closes [Issue #59](https://github.com/PlotPyStack/PlotPy/issues/59))
+* **Z-axis log data update** — Fixed image data not being recomputed when calling `set_data()` while Z-axis log scale is active — the log-transformed data is now refreshed and the LUT range preserved in log mode
+* **`YRangeCursorTool`** — Fixed incorrect inequality display and negative ∆y when the Y-range cursors are inverted (dragging the top cursor below the bottom one). Values are now sorted and ∆y is always positive (closes [Issue #55](https://github.com/PlotPyStack/PlotPy/issues/55))
+* **`CurveStatsTool`** — Replaced `min`/`max`/`mean`/`std`/`sum` with their NaN-safe equivalents (`nanmin`, `nanmax`, `nanmean`, `nanstd`, `nansum`) so that signal statistics are computed correctly when the data contains NaN values
+
+⚙️ Dependencies:
+
+* Bumped minimum PythonQwt version from 0.15 to **0.16** to benefit from the Qt6 performance optimizations (closes [Issue #22](https://github.com/PlotPyStack/PlotPy/issues/22) — see [PythonQwt#93](https://github.com/PlotPyStack/PythonQwt/issues/93) for the full optimization log)

doc/requirements.rst

@@ -14,7 +14,7 @@ The `PlotPy` package requires the following Python modules:
       - >= 3.14.1
       - Automatic GUI generation for easy dataset editing and display
     * - PythonQwt
-      - >= 0.15
+      - >= 0.16
       - Qt plotting widgets for Python
     * - numpy
       - >= 1.22
@@ -26,10 +26,10 @@ The `PlotPy` package requires the following Python modules:
       - >= 0.19
       - Image processing in Python
     * - Pillow
-      -
+      - 
       - Python Imaging Library (fork)
     * - tifffile
-      -
+      - 
       - Read and write TIFF files
 
 Optional modules for GUI support (Qt):
@@ -55,26 +55,32 @@ Optional modules for development:
       - Version
       - Summary
     * - build
-      -
+      - 
       - A simple, correct Python build frontend
     * - babel
-      -
+      - 
       - Internationalization utilities
     * - Coverage
-      -
+      - 
       - Code coverage measurement for Python
     * - Cython
       - >=3.0
       - The Cython compiler for writing C extensions in the Python language.
     * - pylint
-      -
+      - 
       - python code static checker
     * - ruff
-      -
+      - 
       - An extremely fast Python linter and code formatter, written in Rust.
     * - pre-commit
-      -
+      - 
       - A framework for managing and maintaining multi-language pre-commit hooks.
+    * - setuptools
+      - 
+      - Most extensible Python build backend with support for C/C++ extension modules
+    * - wheel
+      - 
+      - Command line tool for manipulating wheel files
 
 Optional modules for building the documentation:
 
@@ -86,19 +92,19 @@ Optional modules for building the documentation:
       - Version
       - Summary
     * - sphinx
-      -
+      - 
       - Python documentation generator
     * - myst_parser
-      -
+      - 
       - An extended [CommonMark](https://spec.commonmark.org/) compliant parser,
     * - sphinx-copybutton
-      -
+      - 
       - Add a copy button to each of your code cells.
     * - sphinx_qt_documentation
-      -
+      - 
       - Plugin for proper resolve intersphinx references for Qt elements
     * - python-docs-theme
-      -
+      - 
       - The Sphinx theme for the CPython docs and related projects
 
 Optional modules for running test suite:
@@ -111,8 +117,8 @@ Optional modules for running test suite:
       - Version
       - Summary
     * - pytest
-      -
+      - 
       - pytest: simple powerful testing with Python
     * - pytest-xvfb
-      -
+      - 
       - A pytest plugin to run Xvfb (or Xephyr/Xvnc) for tests.

plotpy/__init__.py

@@ -20,7 +20,7 @@
 .. _GitHub: https://github.com/PierreRaybaut/plotpy
 """
 
-__version__ = "2.9.0"
+__version__ = "2.10.0"
 __VERSION__ = tuple([int(number) for number in __version__.split(".")])
 
 # --- Important note: DATAPATH and LOCALEPATH are used by guidata.configtools

plotpy/items/__init__.py

@@ -33,6 +33,7 @@
     XYImageFilterItem,
     XYImageItem,
     assemble_imageitems,
+    compute_image_items_original_size,
     compute_trimageitems_original_size,
     get_image_from_plot,
     get_image_from_qrect,

plotpy/items/image/__init__.py

@@ -11,6 +11,7 @@
     Histogram2DItem,
     QuadGridItem,
     assemble_imageitems,
+    compute_image_items_original_size,
     compute_trimageitems_original_size,
     get_image_from_plot,
     get_image_from_qrect,

plotpy/items/image/base.py

@@ -132,6 +132,12 @@ def __init__(
         self._filename = None  # The file this image comes from
 
         self.histogram_cache = None
+
+        # Z-axis logarithmic scale support
+        self._log_data: np.ndarray | None = None
+        self._lin_lut_range: tuple[float, float] | None = None
+        self._is_zaxis_log = False
+
         if data is not None:
             self.set_data(data)
         self.param.update_item(self)
@@ -334,6 +340,15 @@ def get_r_values(self, i0, i1, j0, j1, flag_circle=False):
         """
         return self.get_x_values(i0, i1)
 
+    def _recompute_log_data(self) -> None:
+        """Refresh the cached log10 data from the current ``self.data``.
+
+        Used both when toggling the Z-axis log scale on and when the underlying
+        data is replaced (e.g. via :meth:`set_data`) while the log scale is
+        already active.
+        """
+        self._log_data = np.array(np.log10(self.data.clip(1)), dtype=np.float64)
+
     def set_data(
         self, data: np.ndarray, lut_range: tuple[float, float] | None = None
     ) -> None:
@@ -347,9 +362,15 @@ def set_data(
         self.histogram_cache = None
         self.update_bounds()
         self.update_border()
+        # Refresh the cached log10 data when log scale is active, otherwise the
+        # display would keep using the previous (now stale) log data.
+        if self.get_zaxis_log_state():
+            self._recompute_log_data()
         if not self.param.keep_lut_range:
             if lut_range is not None:
                 _min, _max = lut_range
+            elif self.get_zaxis_log_state():
+                _min, _max = get_nan_range(self._log_data)
             else:
                 _min, _max = get_nan_range(data)
             self.set_lut_range((_min, _max))
@@ -552,6 +573,34 @@ def get_lut_range_full(self) -> tuple[float, float]:
         """
         return get_nan_range(self.data)
 
+    # ---- Z-axis logarithmic scale --------------------------------------------
+    def get_zaxis_log_state(self) -> bool:
+        """Return True if Z-axis is in logarithmic scale"""
+        return self._is_zaxis_log
+
+    def set_zaxis_log_state(self, state: bool) -> None:
+        """Set Z-axis logarithmic scale state
+
+        Args:
+            state: True to enable logarithmic scale, False otherwise
+        """
+        self._is_zaxis_log = state
+        plot = self.plot()
+        if state:
+            self._lin_lut_range = self.get_lut_range()
+            if self._log_data is None:
+                self._recompute_log_data()
+            self.set_lut_range(get_nan_range(self._log_data))
+            dtype = self._log_data.dtype
+        else:
+            self._log_data = None
+            self.set_lut_range(self._lin_lut_range)
+            dtype = self.data.dtype
+        if self.interpolate[0] == INTERP_AA:
+            self.interpolate = (INTERP_AA, self.interpolate[1].astype(dtype))
+        if plot is not None:
+            plot.update_colormap_axis(self)
+
     def get_lut_range_max(self) -> tuple[float, float]:
         """Get maximum range for this dataset
 

plotpy/items/image/misc.py

@@ -577,19 +577,27 @@ def get_items_in_rectangle(
 
 def compute_trimageitems_original_size(
     items: list[TrImageItem],
-    src_w: list[float, float, float, float],
-    src_h: list[float, float, float, float],
+    src_w: float,
+    src_h: float,
 ) -> tuple[float, float]:
     """Compute `TrImageItem` original size from max dx and dy
 
     Args:
         items: List of image items
-        src_w: Source width
-        src_h: Source height
+        src_w: Source width (in plot axis units)
+        src_h: Source height (in plot axis units)
 
     Returns:
         Tuple of original size
+
+    .. note::
+
+        The returned size is always positive: when the source rectangle is
+        defined on a reversed axis, ``src_w`` and/or ``src_h`` may be
+        negative. The original (pixel) size is intrinsically positive,
+        independent of axis orientation.
     """
+    src_w, src_h = abs(src_w), abs(src_h)
     trparams = [item.get_transform() for item in items if isinstance(item, TrImageItem)]
     if trparams:
         dx_max = max([dx for _x, _y, _angle, dx, _dy, _hf, _vf in trparams])
@@ -598,6 +606,81 @@ def compute_trimageitems_original_size(
     return src_w, src_h
 
 
+def compute_image_items_original_size(
+    items: list[BaseImageItem],
+    plot: qwt.plot.QwtPlot,
+    p0: QPointF,
+    p1: QPointF,
+) -> tuple[float, float]:
+    """Compute the **native pixel resolution** of a rectangular selection
+    across the given image items.
+
+    The "Original size" semantics is *original resolution*: the returned
+    size is the number of source pixels that span the selection at the
+    item's native resolution, *independent of axis orientation or scaling*.
+    When the selection is larger than the plotted image, the returned size
+    is consequently larger than the image (the missing area will be padded
+    by the export step). When the selection is smaller, it is smaller in
+    pixels — there is **no** clipping to the image bounding rectangle, so
+    that exporting at "Original size" always preserves the source pixel
+    density.
+
+    Args:
+        plot: Plot
+        items: List of image items in the selection
+        p0: First canvas point (top-left, in canvas coordinates)
+        p1: Second canvas point (bottom-right, in canvas coordinates)
+
+    Returns:
+        Tuple ``(width, height)`` in pixels (always positive). When no
+        compatible item is found, falls back to the absolute axis-units
+        size of the selection.
+    """
+    p0x = plot.invTransform(X_BOTTOM, p0.x())
+    p0y = plot.invTransform(Y_LEFT, p0.y())
+    p1x = plot.invTransform(X_BOTTOM, p1.x() + 1)
+    p1y = plot.invTransform(Y_LEFT, p1.y() + 1)
+    sel_x0, sel_x1 = sorted([p0x, p1x])
+    sel_y0, sel_y1 = sorted([p0y, p1y])
+    sel_w = sel_x1 - sel_x0
+    sel_h = sel_y1 - sel_y0
+    widths: list[float] = []
+    heights: list[float] = []
+    for item in items:
+        data = getattr(item, "data", None)
+        if data is None:
+            continue
+        if isinstance(item, TrImageItem):
+            # Use the item's affine transform (handles rotation and shear)
+            get_pix = item.get_pixel_coordinates
+            try:
+                x0p, y0p = get_pix(sel_x0, sel_y0)
+                x1p, y1p = get_pix(sel_x1, sel_y1)
+            except (ValueError, TypeError, IndexError):
+                continue
+            widths.append(abs(x1p - x0p))
+            heights.append(abs(y1p - y0p))
+        else:
+            # For ImageItem / XYImageItem: convert the (possibly oversized)
+            # selection to pixels via the item's own pixel density. This
+            # avoids ``XYImageItem.get_pixel_coordinates`` clamping to
+            # integer indices and yields oversized values when the
+            # selection extends beyond the image — consistently with the
+            # historical behavior of ``ImageItem``.
+            brect = item.boundingRect()
+            bw = abs(brect.width())
+            bh = abs(brect.height())
+            if bw <= 0 or bh <= 0:
+                continue
+            widths.append(sel_w / bw * data.shape[1])
+            heights.append(sel_h / bh * data.shape[0])
+    if widths:
+        return max(widths), max(heights)
+    # Fallback: axis-units size (always positive)
+    _src_x, _src_y, src_w, src_h = get_plot_qrect(plot, p0, p1).getRect()
+    return abs(src_w), abs(src_h)
+
+
 def get_image_from_qrect(
     plot: BasePlot,
     p0: QPointF,
@@ -636,12 +719,12 @@ def get_image_from_qrect(
     if not items:
         raise TypeError(_("There is no supported image item in current plot."))
     if src_size is None:
-        _src_x, _src_y, src_w, src_h = get_plot_qrect(plot, p0, p1).getRect()
+        destw, desth = compute_image_items_original_size(items, plot, p0, p1)
     else:
         # The only benefit to pass the src_size list is to avoid any
         # rounding error in the transformation computed in `get_plot_qrect`
         src_w, src_h = src_size
-    destw, desth = compute_trimageitems_original_size(items, src_w, src_h)
+        destw, desth = compute_trimageitems_original_size(items, src_w, src_h)
     data = get_image_from_plot(
         plot,
         p0,