Adding ability to change channel once loaded and also handle curve data

.github/workflows/tests.yaml

@@ -29,6 +29,11 @@ jobs:
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
         python-version: ["3.10", "3.11", "3.12"]
+    env:
+      QT_QPA_PLATFORM: offscreen
+      LIBGL_ALWAYS_SOFTWARE: "1"
+      QT_OPENGL: software
+      XDG_RUNTIME_DIR: /tmp
     steps:
       - uses: actions/checkout@v6
       - name: Set up Python

.pylintrc

@@ -220,7 +220,7 @@ ignored-classes=optparse.Values,thread._local,_thread._local
 # (useful for modules/projects where namespaces are manipulated during runtime
 # and thus existing member attributes cannot be deduced by static analysis). It
 # supports qualified module names, as well as Unix pattern matching.
-ignored-modules=
+ignored-modules=qtpy
 
 # Show a hint with possible names when a member name was not found. The aspect
 # of finding the hint is based on edit distance.

README.md

@@ -35,20 +35,17 @@ You can drag and drop your favourite AFM image files directly into the Napari vi
 analysis community have developed over at the [Napari Hub](https://www.napari-hub.org/) to analyse your images using
 open-source software and a GUI!
 
-<!-- @ns-rse : table fails MD060 (https://github.com/DavidAnson/markdownlint/blob/main/doc/md060.md) -->
-<!--           but I can not see/understand why.                                                     -->
-<!-- markdownlint-disable MD060 -->
-
-| File Extension | Supported by AFMReader | Description              |
-| -------------- | ---------------------- | ------------------------ |
-| `.asd`         | ✅                     | High-speed AFM format.   |
-| `.gwy`         | ✅                     | Gwyddion saved format.   |
-| `.ibw`         | ✅                     | Igor binary-wave format. |
-| `.jpk`         | ✅                     | JPK instruments format.  |
-| `.spm`         | ✅                     | Bruker spm format.       |
-| `.stp`         | ✅                     | Homemade stp format.     |
-| `.top`         | ✅                     | Homemade top format.     |
-| `.topostats`   | ✅                     | topostats output format. |
+| File Extension  | Supported by AFMReader | Description              |
+| --------------- | ---------------------- | ------------------------ |
+| `.asd`          | ✅                     | High-speed AFM format.   |
+| `.gwy`          | ✅                     | Gwyddion saved format.   |
+| `.ibw`          | ✅                     | Igor binary-wave format. |
+| `.jpk`          | ✅                     | JPK instruments format.  |
+| `.jpk-qi-image` | ✅                     | JPK instruments format.  |
+| `.spm`          | ✅                     | Bruker spm format.       |
+| `.stp`          | ✅                     | Homemade stp format.     |
+| `.top`          | ✅                     | Homemade top format.     |
+| `.topostats`    | ✅                     | topostats output format. |
 
 <!-- markdownlint-enable MD060 -->
 
@@ -115,12 +112,14 @@ This package should be fairly straight-forward and intuitive to use, requiring y
 
 1. Drag and drop your supported AFM file into the Napari Viewer.
 
-2. Type in the name of the channel you would like to use. You may not need to specify a channel for e.g. `.stp`, or the
-   channel may refer to image key in the `.napari-afmreader` file.\*.
+2. For certain file formats (currently `.jpk-qi-data` and `.bin`), a dialog window will open allowing you to choose
+   special loading parameters for that file.
 
-   \*_Possible channel names will not appear at first due to the order in which AFMReader processes an image. Thus,
-   when provided with an non-existent channel name, the dialogue box will then return a list of possible channels to
-   choose from._
+3. Select the name of the channel you would like to use. You may not need to specify a channel for e.g. `.stp`, or the
+   channel may refer to image key in the `.napari-afmreader` file.
+
+4. Once loaded the channel for the image can be changed to one of the other options using the widget in the dock on
+   the right.
 
 ## Licence
 

napari-afmreader/src/napari_afmreader/_alerts.py

@@ -0,0 +1,112 @@
+"""Module used for providing error alerts in the gui and show/ handle loading messages."""
+
+from qtpy.QtCore import Qt
+from qtpy.QtWidgets import (
+    QApplication,
+    QLabel,
+    QVBoxLayout,
+    QWidget,
+)
+
+
+class LoadingWidget(QWidget):
+    """
+    A semi-transparent overlay for napari viewer.
+
+    Parameters
+    ----------
+    viewer : napari.Viewer
+        The napari viewer instance to attach the overlay to.
+    """
+
+    def __init__(self, viewer):
+        """
+        Initialize the LoadingWidget.
+
+        Parameters
+        ----------
+        viewer : napari.Viewer
+            The napari viewer instance to attach the overlay to.
+        """
+        # Parent to the main napari window so it covers everything
+        super().__init__(viewer.window._qt_window)
+        self.viewer = viewer
+
+        # Make overlay semi-transparent
+        self.setAttribute(Qt.WA_TransparentForMouseEvents, False)
+        self.setStyleSheet("background-color: rgba(0, 0, 0, 120);")
+
+        # Center layout
+        layout = QVBoxLayout()
+        layout.setAlignment(Qt.AlignCenter)
+
+        # Create container with rounded background
+        loading_container = QWidget()
+        loading_container.setStyleSheet("""
+            QWidget {
+                background-color: rgba(40, 40, 40, 240);
+                border-radius: 15px;
+                padding: 30px;
+            }
+        """)
+
+        loading_layout = QVBoxLayout()
+        loading_layout.setAlignment(Qt.AlignCenter)
+
+        self.loading_label = QLabel()
+        self.loading_label.setStyleSheet("""
+            QLabel {
+                color: white;
+                font-size: 18px;
+                font-weight: bold;
+                background-color: transparent;
+            }
+        """)
+        self.loading_label.setAlignment(Qt.AlignCenter)
+
+        loading_layout.addWidget(self.loading_label)
+        loading_container.setLayout(loading_layout)
+
+        layout.addWidget(loading_container)
+        self.setLayout(layout)
+
+        self.message = ""
+
+        self.hide()
+
+    def start(self, message="Loading"):
+        """
+        Show the dialog with a message.
+
+        Parameters
+        ----------
+        message : str, optional
+            The message to display in the loading overlay. Defaults to "Loading".
+        """
+        self.message = message
+        self.loading_label.setText(f"{self.message}")
+
+        # Cover the entire napari window
+        self.setGeometry(self.parent().rect())
+
+        self.show()
+        self.raise_()  # Bring to front
+        QApplication.processEvents()
+
+    def stop(self):
+        """Hide the widget."""
+        self.hide()
+        QApplication.processEvents()
+
+    def resizeEvent(self, event):
+        """
+        Keep overlay covering the parent when window resizes.
+
+        Parameters
+        ----------
+        event : QResizeEvent
+            The resize event from Qt.
+        """
+        if self.parent():
+            self.setGeometry(self.parent().rect())
+        super().resizeEvent(event)