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tomotools
tomoscan
Commits
80f69a28
Commit
80f69a28
authored
Nov 06, 2020
by
payno
Browse files
Revert "Merge branch 'h5py_3_compatibility' into 'master'"
This reverts merge request
!28
parent
b44a4210
Pipeline
#36689
passed with stages
in 3 minutes and 42 seconds
Changes
6
Pipelines
1
Hide whitespace changes
Inline
Side-by-side
.gitlab-ci.yml
View file @
80f69a28
...
...
@@ -19,6 +19,7 @@ check_style:
before_script
:
-
pip install black
script
:
-
pip install -r requirements.txt
# run black
-
LC_ALL=C.UTF-8 black --check --safe .
...
...
@@ -33,14 +34,12 @@ 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
...
...
@@ -67,10 +66,8 @@ doc:
-
export LD_LIBRARY_PATH=/lib/x86_64-linux-gnu/:${LD_LIBRARY_PATH}
-
export ORANGE_WEB_LOG='False'
-
python --version
-
source ./ci/install_scripts.sh
-
python -m pip install pip --upgrade
-
python -m pip install setuptools --upgrade
-
install_silx
-
python -m pip install -r requirements.txt
-
python -m pip install .
script
:
...
...
@@ -98,7 +95,6 @@ test:test-tomoscan-tutorials:
-
export LD_LIBRARY_PATH=/lib/x86_64-linux-gnu/:${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
...
...
@@ -107,7 +103,6 @@ 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
deleted
100644 → 0
View file @
b44a4210
#!/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
View file @
80f69a28
#
silx>=0.
14
silx
>=0.
9
lxml
numpy
\ No newline at end of file
setup.py
View file @
80f69a28
...
...
@@ -321,7 +321,7 @@ def get_project_configuration(dry_run):
install_requires
=
[
# for the script launcher and pkg_resources
"setuptools"
,
"silx>=0.
14a
"
,
"silx>=0.
9
"
,
"lxml"
,
]
...
...
tomoscan/esrf/hdf5scan.py
View file @
80f69a28
...
...
@@ -43,7 +43,6 @@ 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
...
...
@@ -444,9 +443,7 @@ 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
=
h5py_read_dataset
(
h5_file
[
self
.
_entry
][
self
.
_ROTATION_ANGLE_PATH
]
)
_rotation_angles
=
h5_file
[
self
.
_entry
][
self
.
_ROTATION_ANGLE_PATH
][()]
# cast in float
self
.
_rotation_angles
=
tuple
(
[
float
(
angle
)
for
angle
in
_rotation_angles
]
...
...
@@ -458,9 +455,7 @@ 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
=
h5py_read_dataset
(
h5_file
[
self
.
_entry
][
self
.
_IMG_KEY_PATH
]
)
self
.
_image_keys
=
h5_file
[
self
.
_entry
][
self
.
_IMG_KEY_PATH
][()]
return
self
.
_image_keys
@
property
...
...
@@ -469,9 +464,9 @@ 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
py_read_dataset
(
h5_file
[
self
.
_entry
][
self
.
_IMG_KEY_CONTROL_PATH
]
)
self
.
_image_keys_control
=
h5
_file
[
self
.
_entry
][
self
.
_IMG_KEY_CONTROL_PATH
][()]
else
:
self
.
_image_keys_control
=
None
return
self
.
_image_keys_control
...
...
@@ -568,7 +563,7 @@ 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
=
h5py_read_dataset
(
h5_file
[
self
.
_entry
][
self
.
_FOV_PATH
]
)
fov
=
h5_file
[
self
.
_entry
][
self
.
_FOV_PATH
]
[()]
return
_FOV
.
from_value
(
fov
)
else
:
return
None
...
...
@@ -576,9 +571,7 @@ 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
=
h5py_read_dataset
(
h5_file
[
self
.
_entry
][
self
.
_ESTIMATED_COR_FRM_MOTOR_PATH
]
)
value
=
h5_file
[
self
.
_entry
][
self
.
_ESTIMATED_COR_FRM_MOTOR_PATH
][()]
return
float
(
value
)
else
:
return
None
...
...
@@ -783,7 +776,7 @@ 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
=
h5py_read_dataset
(
node
)
value
=
node
[()]
if
"unit"
in
node
.
attrs
:
unit
=
node
.
attrs
[
"unit"
]
elif
"units"
in
node
.
attrs
:
...
...
tomoscan/esrf/mock.py
View file @
80f69a28
...
...
@@ -36,7 +36,6 @@ 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
:
...
...
@@ -294,7 +293,7 @@ class MockHDF5(_ScanMock):
# add data
if
"data"
in
detector_grp
:
# read and remove data
current_dataset
=
h5py_read_dataset
(
detector_grp
[
"data"
]
)
current_dataset
=
detector_grp
[
"data"
]
[()]
new_dataset
=
numpy
.
append
(
current_dataset
,
data_
)
del
detector_grp
[
"data"
]
shape
=
list
(
current_dataset
.
shape
)
...
...
@@ -305,7 +304,7 @@ class MockHDF5(_ScanMock):
# add rotation angle
if
"rotation_angle"
in
sample_grp
:
new_rot_angle
=
h5py_read_dataset
(
sample_grp
[
"rotation_angle"
]
)
new_rot_angle
=
sample_grp
[
"rotation_angle"
]
[()]
new_rot_angle
=
numpy
.
append
(
new_rot_angle
,
rotation_angle
)
del
sample_grp
[
"rotation_angle"
]
else
:
...
...
@@ -315,7 +314,7 @@ class MockHDF5(_ScanMock):
# add image_key
if
"image_key"
in
detector_grp
:
new_image_key
=
h5py_read_dataset
(
detector_grp
[
"image_key"
]
)
new_image_key
=
detector_grp
[
"image_key"
]
[()]
new_image_key
=
numpy
.
append
(
new_image_key
,
image_key
)
del
detector_grp
[
"image_key"
]
else
:
...
...
@@ -325,9 +324,7 @@ class MockHDF5(_ScanMock):
# add image_key_control
if
"image_key_control"
in
detector_grp
:
new_image_key_control
=
h5py_read_dataset
(
detector_grp
[
"image_key_control"
]
)
new_image_key_control
=
detector_grp
[
"image_key_control"
][()]
new_image_key_control
=
numpy
.
append
(
new_image_key_control
,
image_key_control
)
...
...
@@ -339,7 +336,7 @@ class MockHDF5(_ScanMock):
# add count_time
if
"count_time"
in
detector_grp
:
new_count_time
=
h5py_read_dataset
(
detector_grp
[
"count_time"
]
)
new_count_time
=
detector_grp
[
"count_time"
]
[()]
new_count_time
=
numpy
.
append
(
new_count_time
,
self
.
_PROJ_COUNT
)
del
detector_grp
[
"count_time"
]
else
:
...
...
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