Merge pull request #3860 from t20100/silx-view-slicing2

silx view: Added `--slices` option

ci/appveyor.yml

@@ -30,8 +30,8 @@ environment:
           WITH_GL_TEST: True
           PIP_OPTIONS: "-q --pre"
 
-        # Python 3.7
-        - PYTHON_DIR: "C:\\Python37-x64"
+        # Python 3.9
+        - PYTHON_DIR: "C:\\Python39-x64"
           QT_BINDING: "PySide6"
           WITH_GL_TEST: False  # OpenGL not working
           PIP_OPTIONS: "-q --pre"

doc/source/applications/view.rst

@@ -41,25 +41,59 @@ and to view this data in plot widgets or in simple table views.
 Usage
 -----
 
-::
+.. code-block:: none
 
-    silx view [-h] [--debug] [--use-opengl-plot] [files [files ...]]
+    silx view [-h] [--slices SLICES [SLICES ...]] [--debug] [--use-opengl-plot] [-f] [--hdf5-file-locking] [files ...]
 
 
 Options
 -------
 
-  -h, --help           Show this help message and exit
-  --debug              Set logging system in debug mode
-  --use-opengl-plot    Use OpenGL for plots (instead of matplotlib)
-  -f, --fresh          Start the application using new fresh user preferences
-  --hdf5-file-locking  Start the application with HDF5 file locking enabled (it is disabled by default)
+.. code-block:: none
+
+  -h, --help            show this help message and exit
+  --slices SLICES [SLICES ...]
+                        List of slice indices to open (Only for dataset)
+  --debug               Set logging system in debug mode
+  --use-opengl-plot     Use OpenGL for plots (instead of matplotlib)
+  -f, --fresh           Start the application using new fresh user preferences
+  --hdf5-file-locking   Start the application with HDF5 file locking enabled (it is disabled by
+                        default)
 
 Examples of usage
 -----------------
 
-::
+Open file(s)
+............
+
+.. code-block:: none
 
     silx view 31oct98.dat
     silx view *.edf
     silx view myfile.h5
+
+
+Open HDF5 dataset(s)
+....................
+
+Using the HDF5 path to the dataset:
+
+.. code-block:: none
+
+    silx view my_hdf5_file.h5::entry/instrument/detector/data
+
+Using wildcard:
+
+.. code-block:: none
+
+   silx view my_hdf5_file.h5::entry/*/data
+
+
+Open HDF5 dataset slices
+........................
+
+Open first and last slices of datasets:
+
+.. code-block:: none
+
+    silx view my_hdf5_file.h5::entry/*/data --slices 0 -1

src/silx/app/utils/parseutils.py

@@ -22,10 +22,13 @@
 # ############################################################################*/
 """Utils related to parsing"""
 
+from __future__ import annotations
+
 __authors__ = ["V. Valls"]
 __license__ = "MIT"
 __date__ = "28/05/2018"
 
+from collections.abc import Sequence
 import glob
 import logging
 from typing import Generator, Iterable, Union, Any, Optional
@@ -69,14 +72,19 @@ def to_bool(thing: Any, default: Optional[bool]=None) -> bool:
         raise
 
 
-def filenames_to_dataurls(filenames: Iterable[Union[str, Path]]) -> Generator[object, None, None]:
+def filenames_to_dataurls(
+    filenames: Iterable[Union[str, Path]],
+    slices: Sequence[int]=tuple(),
+) -> Generator[object, None, None]:
     """Expand filenames and HDF5 data path in files input argument"""
     # Imports here so they are performed after setting HDF5_USE_FILE_LOCKING and logging level
     import silx.io
     from silx.io.utils import match
     from silx.io.url import DataUrl
     import silx.utils.files
 
+    extra_slices = tuple(slices)
+
     for filename in filenames:
         url = DataUrl(filename)
 
@@ -94,13 +102,21 @@ def filenames_to_dataurls(filenames: Iterable[Union[str, Path]]) -> Generator[ob
             else:
                 data_paths = [url.data_path()]
 
+            if not extra_slices:
+                data_slices = (url.data_slice(),)
+            elif not url.data_slice():
+                data_slices = extra_slices
+            else:
+                data_slices = [tuple(url.data_slice()) + (s,) for s in extra_slices]
+
             for data_path in data_paths:
-                yield DataUrl(
-                    file_path=file_path,
-                    data_path=data_path,
-                    data_slice=url.data_slice(),
-                    scheme=url.scheme(),
-                )
+                for data_slice in data_slices:
+                    yield DataUrl(
+                        file_path=file_path,
+                        data_path=data_path,
+                        data_slice=data_slice,
+                        scheme=url.scheme(),
+                    )
 
 
 def to_enum(thing: Any, enum_type, default: Optional[object]=None):

src/silx/app/view/main.py

@@ -44,6 +44,14 @@ def createParser():
         'files',
         nargs=argparse.ZERO_OR_MORE,
         help='Data file to show (h5 file, edf files, spec files)')
+    parser.add_argument(
+        '--slices',
+        dest='slices',
+        default=tuple(),
+        type=int,
+        nargs='+',
+        help='List of slice indices to open (Only for dataset)',
+    )
     parser.add_argument(
         '--debug',
         dest="debug",
@@ -151,7 +159,7 @@ def sigintHandler(*args):
         # It have to be done after the settings (after the Viewer creation)
         silx.config.DEFAULT_PLOT_BACKEND = "opengl"
 
-    for url in parseutils.filenames_to_dataurls(options.files):
+    for url in parseutils.filenames_to_dataurls(options.files, options.slices):
         # TODO: Would be nice to add a process widget and a cancel button
         try:
             window.appendFile(url.path())

src/silx/gui/data/DataViewer.py

@@ -286,6 +286,10 @@ def __updateDataInView(self):
     def __setDataInView(self):
         self.__currentView.setData(self.__displayedData)
         self.__currentView.setDataSelection(self.__displayedSelection)
+
+        if self.__displayedSelection is None:
+            return
+
         # Emit signal only when selection has changed
         if (self.__previousSelection.slice != self.__displayedSelection.slice or
             self.__previousSelection.permutation != self.__displayedSelection.permutation

src/silx/gui/hdf5/Hdf5TreeModel.py

@@ -38,6 +38,7 @@
 from .Hdf5LoadingItem import Hdf5LoadingItem
 from . import _utils
 from ... import io as silx_io
+from ...io._sliceh5 import DatasetSlice
 
 import h5py
 
@@ -61,6 +62,8 @@ def _createRootLabel(h5obj):
         if path.startswith("/"):
             path = path[1:]
         label = "%s::%s" % (filename, path)
+        if isinstance(h5obj, DatasetSlice):
+            label += str(list(h5obj.indices))
     return label
 
 
@@ -573,9 +576,12 @@ def __areH5pyObjectEqual(obj1, obj2):
         if not isinstance(obj2, type(obj1)):
             return False
         def key(item):
-            if item.file is None:
-                return item.name
-            return item.file.filename, item.file.mode, item.name
+            info = [item.name]
+            if item.file is not None:
+                info += [item.file.filename, item.file.mode]
+            if isinstance(item, DatasetSlice):
+                info.append(item.indices)
+            return tuple(info)
         return key(obj1) == key(obj2)
 
     def h5pyObjectRow(self, h5pyObject):

src/silx/gui/plot/tools/profile/core.py

@@ -1,6 +1,6 @@
 # /*##########################################################################
 #
-# Copyright (c) 2018-2020 European Synchrotron Radiation Facility
+# Copyright (c) 2018-2023 European Synchrotron Radiation Facility
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -37,6 +37,7 @@
 from silx.image.bilinear import BilinearImage
 from silx.gui import qt
 from silx.gui import colors
+import silx.gui.plot.items
 
 
 class CurveProfileData(typing.NamedTuple):
@@ -120,7 +121,7 @@ def invalidateProperties(self):
     def _setPlotItem(self, plotItem):
         """Specify the plot item to use with this profile
 
-        :param `~silx.gui.plot.items.item.Item` plotItem: A plot item
+        :param `~silx.gui.plot.items.Item` plotItem: A plot item
         """
         previousPlotItem = self.getPlotItem()
         if previousPlotItem is plotItem:
@@ -131,7 +132,7 @@ def _setPlotItem(self, plotItem):
     def getPlotItem(self):
         """Returns the plot item used by this profile
 
-        :rtype: `~silx.gui.plot.items.item.Item`
+        :rtype: `~silx.gui.plot.items.Item`
         """
         if self.__plotItem is None:
             return None