tomwer 1.3.5__py3-none-any.whl → 1.3.7__py3-none-any.whl

tomwer/core/scan/blissscan.py

@@ -54,7 +54,7 @@ import logging
 from typing import Optional
 
 from silx.io.utils import h5py_read_dataset
-from tomoscan.io import HDF5File, get_swmr_mode
+from silx.io.utils import open as open_hdf5
 
 _logger = logging.getLogger(__name__)
 
@@ -203,7 +203,7 @@ class BlissScan:
                     return True
             return False
 
-        with HDF5File(file_path, mode="r", swmr=get_swmr_mode()) as h5s:
+        with open_hdf5(file_path) as h5s:
             if not isinstance(h5s, h5py.Group) or not isinstance(
                 h5s[entry], h5py.Group
             ):
@@ -227,7 +227,7 @@ class BlissScan:
             return tuple()
         else:
             res = []
-            with HDF5File(file_path, mode="r", swmr=get_swmr_mode()) as h5s:
+            with open_hdf5(file_path) as h5s:
                 for entry in h5s:
                     if BlissScan.is_bliss_valid_entry(file_path=file_path, entry=entry):
                         res.append(entry)

tomwer/core/scan/nxtomoscan.py

@@ -40,12 +40,12 @@ from urllib.parse import urlparse
 
 import h5py
 from processview.core.dataset import DatasetIdentifier
+from silx.io.utils import open as open_hdf5
 from tomoscan.esrf.identifier.hdf5Identifier import (
     NXtomoScanIdentifier as _NXtomoScanIdentifier,
 )
 from tomoscan.esrf.identifier.url_utils import UrlSettings, split_path, split_query
 from tomoscan.esrf.scan.nxtomoscan import NXtomoScan as _tsNXtomoScan
-from tomoscan.io import HDF5File, get_swmr_mode
 from nxtomo.nxobject.nxdetector import ImageKey
 
 from tomwer.utils import docstring
@@ -424,7 +424,7 @@ class NXtomoScan(_tsNXtomoScan, TomwerScanBase):
             return tuple()
         else:
             res = []
-            with HDF5File(file_path, mode="r", swmr=get_swmr_mode()) as h5s:
+            with open_hdf5(file_path) as h5s:
                 for entry_name, node in h5s.items():
                     if isinstance(node, h5py.Group):
                         if NXtomoScan.entry_is_nx_tomo(node):

tomwer/core/scan/scanbase.py

@@ -40,8 +40,9 @@ import functools
 import numpy
 from silx.io.url import DataUrl
 from silx.utils.enum import Enum as _Enum
+from silx.io.utils import open as open_hdf5
+
 from tomoscan.identifier import VolumeIdentifier
-from tomoscan.io import HDF5File, get_swmr_mode
 from tomoscan.normalization import IntensityNormalization
 from tomoscan.volumebase import VolumeBase
 from tomoscan.identifier import BaseIdentifier
@@ -131,7 +132,7 @@ class TomwerScanBase(TomwerObject):
             and self.process_file is not None
             and os.path.exists(self.process_file)
         ):
-            with HDF5File(self.process_file, mode="r", swmr=get_swmr_mode()) as h5s:
+            with open_hdf5(self.process_file) as h5s:
                 self._process_index = len(h5s.items())
         else:
             self._process_index = 0
@@ -756,7 +757,7 @@ class TomwerScanBase(TomwerObject):
         from tomwer.core.process.task import Task
 
         if os.path.exists(self.process_file):
-            with HDF5File(self.process_file, mode="r", swmr=get_swmr_mode()) as h5s:
+            with open_hdf5(self.process_file) as h5s:
                 if not hasattr(self, "entry"):
                     entry = "entry"
                 else:
@@ -864,9 +865,7 @@ def _get_reconstructed_single_file_volume(
 
                 if check_url is True:
                     try:
-                        with HDF5File(
-                            os.path.abspath(file_), "r", swmr=get_swmr_mode()
-                        ) as h5f:
+                        with open_hdf5(os.path.abspath(file_)) as h5f:
                             if entry not in h5f:
                                 logger.info("{volume} does not exists")
                                 return None

tomwer/core/utils/test/test_image.py

@@ -0,0 +1,30 @@
+import numpy
+import pytest
+
+from tomwer.core.utils.image import ImageScaleMethod, scale_img2_to_img1, shift_img
+
+
+@pytest.mark.parametrize(
+    "use_scipy, dx, dy, cval", ((True, 1.0, -2.3, 0), (False, 0.0, 3.6, 2))
+)
+def test_shift_image(use_scipy, dx, dy, cval):
+    data = numpy.linspace(0, 12, 100 * 100).reshape(100, 100)
+    assert isinstance(
+        shift_img(data=data, dx=dx, dy=dy, cval=cval, use_scipy=use_scipy),
+        numpy.ndarray,
+    )
+
+
+def test_scale_img2_to_img1():
+    """
+    test scale_img2_to_img1 function
+    """
+    img_1 = numpy.linspace(0, 10, 100 * 100, dtype=numpy.float16).reshape(100, 100)
+    img_2 = numpy.linspace(20, 100, 100 * 100, dtype=numpy.float16).reshape(100, 100)
+
+    rescale_img = scale_img2_to_img1(img_2, img_1, method=ImageScaleMethod.MEAN)
+    numpy.testing.assert_array_almost_equal(
+        img_2,
+        rescale_img,
+        decimal=1,
+    )

tomwer/core/utils/test/test_nxtomo.py

@@ -0,0 +1,66 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016-2017 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
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+
+__authors__ = ["H. Payno"]
+__license__ = "MIT"
+__date__ = "02/12/2021"
+
+
+import pytest
+from nxtomo.nxobject.nxdetector import ImageKey
+
+from tomwer.core.utils.nxtomoutils import get_n_series
+
+
+def test_get_n_series():
+    """test tomwer.core.utils.nxtomoutils.get_n_series function"""
+    array_1 = (
+        [ImageKey.DARK_FIELD] * 2
+        + [ImageKey.FLAT_FIELD]
+        + [ImageKey.PROJECTION] * 4
+        + [ImageKey.FLAT_FIELD]
+    )
+
+    with pytest.raises(ValueError):
+        get_n_series(array_1, ImageKey.INVALID)
+    with pytest.raises(ValueError):
+        get_n_series(array_1, 3)
+
+    assert len(array_1) == 8
+    assert get_n_series(array_1, ImageKey.DARK_FIELD) == 1
+    assert get_n_series(array_1, ImageKey.FLAT_FIELD) == 2
+    assert get_n_series(array_1, ImageKey.PROJECTION) == 1
+    assert get_n_series(array_1, 0) == 1
+
+    array_2 = (
+        [ImageKey.FLAT_FIELD.value]
+        + [ImageKey.PROJECTION.value] * 4
+        + [ImageKey.INVALID.value] * 2
+        + [ImageKey.PROJECTION.value] * 3
+        + [ImageKey.FLAT_FIELD.value]
+    )
+    assert get_n_series(array_2, ImageKey.DARK_FIELD) == 0
+    assert get_n_series(array_2, ImageKey.PROJECTION) == 1
+    assert get_n_series(array_2, ImageKey.FLAT_FIELD) == 2

tomwer/core/utils/test/test_scan_utils.py

@@ -0,0 +1,46 @@
+import os
+
+from tomwer.core.scan.blissscan import BlissScan
+from tomwer.core.scan.edfscan import EDFTomoScan
+from tomwer.core.scan.nxtomoscan import NXtomoScan
+from tomwer.core.utils.scanutils import format_output_location
+
+
+def test_format_output_location(tmp_path):
+    """
+    test different use cases of 'format_output_location'
+    """
+    bliss_raw_dir = tmp_path / "raw"
+    bliss_raw_dir.mkdir()
+    bliss_sample_dir = bliss_raw_dir / "sample"
+    bliss_sample_dir.mkdir()
+    bliss_master_file = bliss_sample_dir / "dataset.h5"
+
+    bliss_proposal_file = bliss_raw_dir / "ihsample.h5"
+    bliss_proposal_file = os.path.abspath(bliss_proposal_file)
+
+    bliss_scan = BlissScan(
+        master_file=bliss_master_file, entry="1.1", proposal_file=bliss_proposal_file
+    )
+    expected_path = os.path.join(tmp_path, "reduced", "sample")
+    assert (
+        format_output_location(
+            location="{scan_parent_dir_basename}/../reduced/{scan_dir_name}",
+            scan=bliss_scan,
+        )
+        == expected_path
+    )
+
+    edf_scan = EDFTomoScan("/test/my/folder/")
+    assert (
+        format_output_location(
+            location="{scan_parent_dir_basename}/output", scan=edf_scan
+        )
+        == "/test/my/output"
+    )
+
+    hdf5_scan = NXtomoScan("/ddsad/my/file.hdf5", entry="entry0000")
+    assert (
+        format_output_location(location="{scan_basename}/output.nx", scan=hdf5_scan)
+        == "/ddsad/my/output.nx"
+    )

tomwer/core/utils/test/test_time.py

@@ -0,0 +1,6 @@
+from tomwer.core.utils.time import Timer
+
+
+def test_timer():
+    with Timer("timer name"):
+        pass

tomwer/core/volume/test/test_volumes.py

@@ -0,0 +1,21 @@
+from tomwer.core.volume import EDFVolume, HDF5Volume, RawVolume
+from tomwer.core.volume.rawvolume import RawVolumeIdentifier
+
+
+def test_volume_data_parent_folder():
+    edf_volume = EDFVolume(folder="/my/folder/path")
+    assert edf_volume.volume_data_parent_folder() == "/my/folder"
+
+    hdf5_volume = HDF5Volume(file_path="/path/to/hdf5/file.hdf5", data_path="entry")
+    assert hdf5_volume.volume_data_parent_folder() == "/path/to/hdf5"
+
+    raw_volume = RawVolume(file_path="/path/to/raw.vol")
+    assert raw_volume.volume_data_parent_folder() == "/path/to"
+
+
+def test_raw_identifier():
+    raw_volume = RawVolume(file_path="/path/to/raw.vol")
+    assert (
+        RawVolumeIdentifier.from_str(raw_volume.get_identifier().to_str())
+        == raw_volume.get_identifier()
+    )

tomwer/gui/control/reducedarkflatselector.py

@@ -8,11 +8,11 @@ from silx.gui import qt
 from silx.gui.plot import Plot2D
 from silx.io.dictdump import h5todict
 from silx.io.url import DataUrl
+from silx.io.utils import open as open_hdf5
 from silx.gui.dialog.DataFileDialog import DataFileDialog
 
 from tomoscan.esrf.scan.utils import cwd_context
 from tomoscan.framereducer.target import REDUCER_TARGET
-from tomoscan.io import HDF5File, get_swmr_mode
 
 from tomwer.io.utils import get_default_directory
 
@@ -249,7 +249,7 @@ class ReduceDarkFlatSelectorTableWidget(qt.QWidget):
         if not os.path.exists(file_path):
             _logger.error(f"file doesn't exists ({file_path})")
 
-        with HDF5File(file_path, mode="r", swmr=get_swmr_mode()) as h5f:
+        with open_hdf5(file_path) as h5f:
             entries = tuple(h5f.keys())
 
         res = []