Merge branch 'h5py_3_compatibility' into 'master'

H5py 3 compatibility

See merge request !28

.gitlab-ci.yml

@@ -19,7 +19,6 @@ check_style:
   before_script:
     - pip install black
   script:
-    - pip install -r requirements.txt
     # run black
     - LC_ALL=C.UTF-8 black --check --safe .
 
@@ -34,12 +33,14 @@ doc:
     - arch
     - which python
     - python --version
+    - source ./ci/install_scripts.sh
     - python -m pip install pip --upgrade
     - python -m pip install setuptools --upgrade
     - python -m pip install sphinx
     - python -m pip install nbsphinx
     - python -m pip install nbconvert
     - python -m pip install pandoc
+    - install_silx
     - python -m pip install -r requirements.txt
     - rm -rf artifacts
     - mkdir artifacts
@@ -66,8 +67,10 @@ doc:
     - export LD_LIBRARY_PATH=/lib/x86_64-linux-gnu/:${LD_LIBRARY_PATH}
     - export ORANGE_WEB_LOG='False'
     - python --version
+    - source ./ci/install_scripts.sh
     - python -m pip install pip --upgrade
     - python -m pip install setuptools --upgrade
+    - install_silx
     - python -m pip install -r requirements.txt
     - python -m pip install .
   script:
@@ -95,6 +98,7 @@ test:test-tomoscan-tutorials:
     - export LD_LIBRARY_PATH=/lib/x86_64-linux-gnu/:${LD_LIBRARY_PATH}
     - export ORANGE_WEB_LOG='False'
     - python --version
+    - source ./ci/install_scripts.sh
     - python -m pip install pip --upgrade
     - python -m pip install setuptools --upgrade
     - python -m pip install numpy --upgrade
@@ -103,6 +107,7 @@ test:test-tomoscan-tutorials:
     - python -m pip install nbconvert
     - python -m pip install pandoc
     - python -m pip install ipykernel
+    - install_silx
     - python -m pip install -r requirements.txt
     - python -m pip install fabio --upgrade --pre
     - python -m pip install silx --upgrade --pre

ci/install_scripts.sh

+#!/bin/bash
+
+function install_silx(){
+
+    if [ "$2" = 'latest' ]; then
+        python -m install silx
+    else
+        python -m pip install git+https://github.com/silx-kit/silx.git
+    fi
+}
+
+
+function silx_version(){
+    python -c 'import silx; print(silx.version)'
+}

requirements.txt

-silx>=0.9
+# silx>=0.14
 lxml
 numpy
\ No newline at end of file

setup.py

@@ -321,7 +321,7 @@ def get_project_configuration(dry_run):
     install_requires = [
         # for the script launcher and pkg_resources
         "setuptools",
-        "silx>=0.9",
+        "silx>=0.14a",
         "lxml",
     ]
 

tomoscan/esrf/hdf5scan.py

@@ -43,6 +43,7 @@ from tomoscan.io import HDF5File
 from silx.io.utils import get_data
 from ..unitsystem import metricsystem
 from .utils import get_compacted_dataslices
+from silx.io.utils import h5py_read_dataset
 import typing
 import logging
 
@@ -443,7 +444,9 @@ class HDF5TomoScan(TomoScanBase):
         if self._rotation_angles is None:
             self._check_hdf5scan_validity()
             with HDF5File(self.master_file, "r", swmr=True) as h5_file:
-                _rotation_angles = h5_file[self._entry][self._ROTATION_ANGLE_PATH][()]
+                _rotation_angles = h5py_read_dataset(
+                    h5_file[self._entry][self._ROTATION_ANGLE_PATH]
+                )
                 # cast in float
                 self._rotation_angles = tuple(
                     [float(angle) for angle in _rotation_angles]
@@ -455,7 +458,9 @@ class HDF5TomoScan(TomoScanBase):
         if self._entry and self._image_keys is None:
             self._check_hdf5scan_validity()
             with HDF5File(self.master_file, "r", swmr=True) as h5_file:
-                self._image_keys = h5_file[self._entry][self._IMG_KEY_PATH][()]
+                self._image_keys = h5py_read_dataset(
+                    h5_file[self._entry][self._IMG_KEY_PATH]
+                )
         return self._image_keys
 
     @property
@@ -464,9 +469,9 @@ class HDF5TomoScan(TomoScanBase):
             self._check_hdf5scan_validity()
             with HDF5File(self.master_file, "r", swmr=True) as h5_file:
                 if self._IMG_KEY_CONTROL_PATH in h5_file[self._entry]:
-                    self._image_keys_control = h5_file[self._entry][
-                        self._IMG_KEY_CONTROL_PATH
-                    ][()]
+                    self._image_keys_control = h5py_read_dataset(
+                        h5_file[self._entry][self._IMG_KEY_CONTROL_PATH]
+                    )
                 else:
                     self._image_keys_control = None
         return self._image_keys_control
@@ -563,7 +568,7 @@ class HDF5TomoScan(TomoScanBase):
     def _get_fov(self):
         with HDF5File(self.master_file, "r", swmr=True, libver="latest") as h5_file:
             if self._FOV_PATH in h5_file[self._entry]:
-                fov = h5_file[self._entry][self._FOV_PATH][()]
+                fov = h5py_read_dataset(h5_file[self._entry][self._FOV_PATH])
                 return _FOV.from_value(fov)
             else:
                 return None
@@ -571,7 +576,9 @@ class HDF5TomoScan(TomoScanBase):
     def _get_estimated_cor_frm_motor(self):
         with HDF5File(self.master_file, "r", swmr=True, libver="latest") as h5_file:
             if self._ESTIMATED_COR_FRM_MOTOR_PATH in h5_file[self._entry]:
-                value = h5_file[self._entry][self._ESTIMATED_COR_FRM_MOTOR_PATH][()]
+                value = h5py_read_dataset(
+                    h5_file[self._entry][self._ESTIMATED_COR_FRM_MOTOR_PATH]
+                )
                 return float(value)
             else:
                 return None
@@ -776,7 +783,7 @@ class HDF5TomoScan(TomoScanBase):
         Unit can be defined in on of the group attributes. It it is the case
         will pick this unit, otherwise will use the default unit
         """
-        value = node[()]
+        value = h5py_read_dataset(node)
         if "unit" in node.attrs:
             unit = node.attrs["unit"]
         elif "units" in node.attrs:

tomoscan/esrf/mock.py

@@ -36,6 +36,7 @@ from xml.etree import cElementTree
 import fabio
 import fabio.edfimage
 from .hdf5scan import ImageKey, HDF5TomoScan
+from silx.io.utils import h5py_read_dataset
 
 
 class _ScanMock:
@@ -293,7 +294,7 @@ class MockHDF5(_ScanMock):
             # add data
             if "data" in detector_grp:
                 # read and remove data
-                current_dataset = detector_grp["data"][()]
+                current_dataset = h5py_read_dataset(detector_grp["data"])
                 new_dataset = numpy.append(current_dataset, data_)
                 del detector_grp["data"]
                 shape = list(current_dataset.shape)
@@ -304,7 +305,7 @@ class MockHDF5(_ScanMock):
 
             # add rotation angle
             if "rotation_angle" in sample_grp:
-                new_rot_angle = sample_grp["rotation_angle"][()]
+                new_rot_angle = h5py_read_dataset(sample_grp["rotation_angle"])
                 new_rot_angle = numpy.append(new_rot_angle, rotation_angle)
                 del sample_grp["rotation_angle"]
             else:
@@ -314,7 +315,7 @@ class MockHDF5(_ScanMock):
 
             # add image_key
             if "image_key" in detector_grp:
-                new_image_key = detector_grp["image_key"][()]
+                new_image_key = h5py_read_dataset(detector_grp["image_key"])
                 new_image_key = numpy.append(new_image_key, image_key)
                 del detector_grp["image_key"]
             else:
@@ -324,7 +325,9 @@ class MockHDF5(_ScanMock):
 
             # add image_key_control
             if "image_key_control" in detector_grp:
-                new_image_key_control = detector_grp["image_key_control"][()]
+                new_image_key_control = h5py_read_dataset(
+                    detector_grp["image_key_control"]
+                )
                 new_image_key_control = numpy.append(
                     new_image_key_control, image_key_control
                 )
@@ -336,7 +339,7 @@ class MockHDF5(_ScanMock):
 
             # add count_time
             if "count_time" in detector_grp:
-                new_count_time = detector_grp["count_time"][()]
+                new_count_time = h5py_read_dataset(detector_grp["count_time"])
                 new_count_time = numpy.append(new_count_time, self._PROJ_COUNT)
                 del detector_grp["count_time"]
             else: