Clarified support for ImageIO based file formats

Author: PierreRaybaut

CHANGELOG.md

@@ -1,7 +1,6 @@
 # Changelog #
 
-See DataLab [roadmap page](https://datalab-platform.com/en/contributing/roadmap.html)
-for future and past milestones.
+See DataLab [roadmap page](https://datalab-platform.com/en/contributing/roadmap.html) for future and past milestones.
 
 ## DataLab Version 0.16.2 ##
 
@@ -27,8 +26,8 @@ This release requires PlotPy v2.4.0 or later, which brings the following bug fix
 ℹ️ Minor new features and enhancements:
 
 * Image file types:
-  * Added native support for reading .SPE, .GEL, .NTPI and .REC image files
-  * Added support for any `imageio`-supported file format through configuration file (entry `imageio_formats` may be customized to complement the default list of supported formats: see `cdl.core.io.image.formats.IMAGEIO_FORMATS_INFO`)
+  * Added native support for reading .SPE, .GEL, .NDPI and .REC image files
+  * Added support for any `imageio`-supported file format through configuration file (entry `imageio_formats` may be customized to complement the default list of supported formats: see [documentation](https://datalab-platform.com/en/features/image/menu_file.html#open-image) for more details)
 
 🛠️ Bug fixes:
 

cdl/config.py

@@ -462,3 +462,17 @@ def reset():
 
 PLOTPY_CONF.update_defaults(PLOTPY_DEFAULTS)
 PLOTPY_CONF.set_application(osp.join(APP_NAME, "plotpy"), CONF_VERSION, load=False)
+
+
+# Default image file formats supported by the ImageIO library
+#
+# This object represents the natively supported image file formats from the ImageIO
+# library. This list is used in the core I/O module to load data from files with the
+# supported formats. It may be extended using the `imageio_formats` option in the
+# configuration file (see section `io`).
+IMAGEIO_FORMATS = (
+    ("*.gel", "Opticks GEL"),
+    ("*.spe", "Princeton Instruments SPE"),
+    ("*.ndpi", "Hamamatsu Slide Scanner NDPI"),
+    ("*.rec", "PCO Camera REC"),
+)

cdl/core/io/image/formats.py

@@ -14,7 +14,7 @@
 import scipy.io as sio
 import skimage.io
 
-from cdl.config import Conf, _
+from cdl.config import IMAGEIO_FORMATS, Conf, _
 from cdl.core.io.base import FormatInfo
 from cdl.core.io.conv import convert_array_to_standard_type
 from cdl.core.io.image import funcs
@@ -216,18 +216,10 @@ def read_data(filename: str) -> np.ndarray:
         return funcs.imread_sif(filename)
 
 
-IMAGEIO_FORMATS_INFO = (
-    ("*.gel", "Opticks GEL"),
-    ("*.spe", "Princeton Instruments SPE"),
-    ("*.ndpi", "Hamamatsu Slide Scanner NDPI"),
-    ("*.rec", "PCO Camera REC"),
-)
-
-
 # Generate classes based on the information above:
 def generate_imageio_format_classes():
     """Generate classes based on the information above"""
-    imageio_formats = IMAGEIO_FORMATS_INFO
+    imageio_formats = IMAGEIO_FORMATS
     conf_formats = Conf.io.imageio_formats.get()
     if conf_formats:
         imageio_formats += conf_formats

doc/features/image/menu_file.rst

@@ -69,13 +69,30 @@ Create a new image from the following supported filetypes:
       - .sif
     * - Princeton Instruments SPE files
       - .spe
+    * - Opticks GEL files
+      - .gel
+    * - Hammamatsu NDPI files
+      - .ndpi
+    * - PCO Camera REC files
+      - .rec
     * - SPIRICON files
       - .scor-data
     * - FXD files
       - .fxd
     * - Bitmap images
       - .bmp
 
+.. note::
+
+    DataLab also supports any image format that can be read by the `imageio` library,
+    provided that the associated plugin(s) are installed (see `imageio documentation <https://imageio.readthedocs.io/en/stable/formats/index.html>`_)
+    and that the output NumPy array data type and shape are supported by DataLab.
+
+    To add a new file format, you may use the `imageio_formats` entry of DataLab configuration file.
+    This entry is a formatted like the `IMAGEIO_FORMATS` object which represents the natively supported formats:
+
+    .. autodata:: cdl.config.IMAGEIO_FORMATS
+
 Save image
 ^^^^^^^^^^