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tomotools
nxtomomill
Commits
3b2352e0
Commit
3b2352e0
authored
Nov 30, 2021
by
payno
Browse files
Merge branch 'benefit_from_validator' into 'master'
benefit from validator and improve tests See merge request
!81
parents
0e1ce57f
4ce926d4
Pipeline
#60804
passed with stages
in 6 minutes and 25 seconds
Changes
5
Pipelines
2
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Inline
Side-by-side
nxtomomill/app/test/test_patch_nx_app.py
View file @
3b2352e0
...
...
@@ -54,8 +54,8 @@ def test_patch_nx_application():
n_proj
=
nproj
,
n_ini_proj
=
nproj
,
create_ini_dark
=
False
,
create_ini_
ref
=
False
,
create_final_
ref
=
False
,
create_ini_
flat
=
False
,
create_final_
flat
=
False
,
dim
=
dim
,
).
scan
main
(
...
...
nxtomomill/converter/dxfile/test_dxfile.py
View file @
3b2352e0
...
...
@@ -37,6 +37,7 @@ from nxtomomill import converter
from
tomoscan.esrf.hdf5scan
import
HDF5TomoScan
from
nxtomomill.test.utils.dxfile
import
MockDxFile
from
silx.io.utils
import
get_data
from
tomoscan.validator
import
is_valid_for_reconstruction
class
TestDxToNxConverter
(
unittest
.
TestCase
):
...
...
@@ -83,6 +84,7 @@ class TestDxToNxConverter(unittest.TestCase):
self
.
assertEqual
(
len
(
scan
.
flats
),
self
.
n_flats
)
self
.
assertEqual
(
numpy
.
array
(
scan
.
rotation_angle
).
min
(),
0
)
self
.
assertEqual
(
numpy
.
array
(
scan
.
rotation_angle
).
max
(),
180
)
assert
is_valid_for_reconstruction
(
scan
)
# check arrays are correctly copied from mock
numpy
.
testing
.
assert_array_equal
(
...
...
nxtomomill/converter/edf/test/test_edf2nx.py
View file @
3b2352e0
...
...
@@ -36,6 +36,7 @@ from tomoscan.esrf.mock import MockEDF
from
tomoscan.esrf.hdf5scan
import
HDF5TomoScan
from
tomoscan.esrf.edfscan
import
EDFTomoScan
from
tomoscan
import
version
from
tomoscan.validator
import
is_valid_for_reconstruction
from
nxtomomill.utils
import
Progress
import
pytest
...
...
@@ -75,3 +76,4 @@ def test_edf_to_nx_converter(progress):
assert
len
(
hdf5_scan
.
alignment_projections
)
==
n_alignment_proj
assert
hdf5_scan
.
dim_1
==
dim
assert
hdf5_scan
.
dim_2
==
dim
assert
is_valid_for_reconstruction
(
hdf5_scan
)
nxtomomill/converter/hdf5/test/test_hdf5converter.py
View file @
3b2352e0
...
...
@@ -41,6 +41,7 @@ from nxtomomill.converter.hdf5.acquisition.baseacquisition import EntryReader
from
nxtomomill.converter.hdf5.acquisition.baseacquisition
import
DatasetReader
from
nxtomomill.io.config
import
TomoHDF5Config
from
tomoscan.esrf.hdf5scan
import
HDF5TomoScan
from
tomoscan.validator
import
is_valid_for_reconstruction
from
nxtomomill.test.utils.bliss
import
MockBlissAcquisition
from
silx.io.url
import
DataUrl
from
silx.io.utils
import
get_data
...
...
@@ -70,11 +71,13 @@ def url_has_been_copied(file_path: str, url: DataUrl):
class
TestH5ToNxConverter
(
unittest
.
TestCase
):
def
setUp
(
self
)
->
None
:
super
().
setUp
()
self
.
folder
=
tempfile
.
mkdtemp
()
self
.
config
=
TomoHDF5Config
()
def
tearDown
(
self
)
->
None
:
shutil
.
rmtree
(
self
.
folder
)
super
().
tearDown
()
def
test_simple_converter_with_nx_detector_attr
(
self
):
"""
...
...
@@ -286,6 +289,7 @@ class TestH5ToNxConverter(unittest.TestCase):
scan
=
HDF5TomoScan
(
scan
=
res_tuple
[
0
],
entry
=
res_tuple
[
1
])
if
hasattr
(
scan
,
"z_translation"
):
self
.
assertTrue
(
scan
.
z_translation
is
not
None
)
self
.
assertTrue
(
is_valid_for_reconstruction
(
scan
))
def
test_ignore_sub_entries
(
self
):
"""
...
...
@@ -389,12 +393,14 @@ class TestDetectorDetection(unittest.TestCase):
class
TestXRDCTConversion
(
unittest
.
TestCase
):
def
setUp
(
self
)
->
None
:
super
().
setUp
()
self
.
folder
=
tempfile
.
mkdtemp
()
self
.
config
=
TomoHDF5Config
()
self
.
config
.
format
=
Format
.
XRD_CT
def
tearDown
(
self
)
->
None
:
shutil
.
rmtree
(
self
.
folder
)
super
().
tearDown
()
def
test_simple_converter_with_nx_detector_attr
(
self
):
"""
...
...
@@ -442,6 +448,7 @@ class TestStandardAcqConversionWithExternalUrls(unittest.TestCase):
"""Test conversion when frames are provided from urls"""
def
setUp
(
self
)
->
None
:
super
().
setUp
()
self
.
folder
=
tempfile
.
mkdtemp
()
self
.
config
=
TomoHDF5Config
()
self
.
config
.
output_file
=
os
.
path
.
join
(
self
.
folder
,
"output.nx"
)
...
...
@@ -468,6 +475,7 @@ class TestStandardAcqConversionWithExternalUrls(unittest.TestCase):
def
tearDown
(
self
)
->
None
:
shutil
.
rmtree
(
self
.
folder
)
super
().
tearDown
()
def
test_dataset_1
(
self
):
"""test a conversion where projections are contained in the
...
...
@@ -497,18 +505,20 @@ class TestStandardAcqConversionWithExternalUrls(unittest.TestCase):
url
=
DataUrl
(
file_path
=
dark_flat_file
,
data_path
=
"/3.1"
,
scheme
=
"silx"
),
),
)
converter
.
from_h5_to_nx
(
configuration
=
self
.
config
,
)
self
.
assertTrue
(
os
.
path
.
exists
(
self
.
config
.
output_file
))
self
.
assertTrue
(
os
.
path
.
exists
(
self
.
config
.
output_file
),
"output file does not exists"
)
with
h5py
.
File
(
self
.
config
.
output_file
,
mode
=
"r"
)
as
h5s
:
self
.
assertEqual
(
len
(
h5s
.
items
()),
1
)
self
.
assertTrue
(
"entry0000"
in
h5s
)
scan
=
HDF5TomoScan
(
scan
=
self
.
config
.
output_file
,
entry
=
"entry0000"
)
self
.
assertTrue
(
is_valid_for_reconstruction
(
scan
))
# check the `data`has been created
self
.
assertTrue
(
len
(
scan
.
projections
),
20
)
...
...
@@ -603,6 +613,7 @@ class TestStandardAcqConversionWithExternalUrls(unittest.TestCase):
self
.
assertEqual
(
vs
.
file_name
,
"acqui_1/sample_0/sample_0.h5"
)
scan
=
HDF5TomoScan
(
scan
=
self
.
config
.
output_file
,
entry
=
"entry0000"
)
self
.
assertTrue
(
is_valid_for_reconstruction
(
scan
))
# check the `data`has been created
self
.
assertTrue
(
len
(
scan
.
projections
),
40
)
...
...
@@ -703,6 +714,7 @@ class TestZSeriesConversionWithExternalUrls(unittest.TestCase):
"""
def
setUp
(
self
)
->
None
:
super
().
setUp
()
self
.
folder
=
tempfile
.
mkdtemp
()
self
.
config
=
TomoHDF5Config
()
...
...
@@ -739,6 +751,7 @@ class TestZSeriesConversionWithExternalUrls(unittest.TestCase):
def
tearDown
(
self
)
->
None
:
shutil
.
rmtree
(
self
.
folder
)
super
().
tearDown
()
def
test_dataset_zseries
(
self
):
"""Test a zseries with only external scan entries"""
...
...
nxtomomill/test/test_utils.py
View file @
3b2352e0
...
...
@@ -58,8 +58,8 @@ class BaseTestAddDarkAndFlats(unittest.TestCase):
n_proj
=
self
.
nproj
,
n_ini_proj
=
self
.
nproj
,
create_ini_dark
=
False
,
create_ini_
ref
=
False
,
create_final_
ref
=
False
,
create_ini_
flat
=
False
,
create_final_
flat
=
False
,
dim
=
self
.
dim
,
).
scan
with
h5py
.
File
(
self
.
_simple_nx
.
master_file
,
mode
=
"r"
)
as
h5s
:
...
...
@@ -73,8 +73,8 @@ class BaseTestAddDarkAndFlats(unittest.TestCase):
n_proj
=
0
,
n_ini_proj
=
0
,
create_ini_dark
=
False
,
create_ini_
ref
=
False
,
create_final_
ref
=
False
,
create_ini_
flat
=
False
,
create_final_
flat
=
False
,
dim
=
self
.
dim
,
).
scan
self
.
_create_vds
(
...
...
@@ -94,8 +94,8 @@ class BaseTestAddDarkAndFlats(unittest.TestCase):
n_proj
=
0
,
n_ini_proj
=
0
,
create_ini_dark
=
False
,
create_ini_
ref
=
False
,
create_final_
ref
=
False
,
create_ini_
flat
=
False
,
create_final_
flat
=
False
,
dim
=
self
.
dim
,
).
scan
self
.
_create_vds
(
...
...
@@ -852,8 +852,8 @@ class TestChangeImageKeyControl(unittest.TestCase):
n_proj
=
self
.
nproj
,
n_ini_proj
=
self
.
nproj
,
create_ini_dark
=
True
,
create_ini_
ref
=
True
,
create_final_
ref
=
True
,
create_ini_
flat
=
True
,
create_final_
flat
=
True
,
dim
=
self
.
dim
,
n_refs
=
4
,
)
...
...
@@ -1096,8 +1096,8 @@ class TestAddDarkAndFlatFromADifferentFolderWithVDS(unittest.TestCase):
n_proj
=
10
,
n_ini_proj
=
2
,
create_ini_dark
=
False
,
create_ini_
ref
=
False
,
create_final_
ref
=
False
,
create_ini_
flat
=
False
,
create_final_
flat
=
False
,
dim
=
self
.
dim
,
).
scan
# 1. add first level of indirection for dark and flat and check the VDS
...
...
@@ -1123,8 +1123,8 @@ class TestAddDarkAndFlatFromADifferentFolderWithVDS(unittest.TestCase):
n_proj
=
10
,
n_ini_proj
=
2
,
create_ini_dark
=
False
,
create_ini_
ref
=
False
,
create_final_
ref
=
False
,
create_ini_
flat
=
False
,
create_final_
flat
=
False
,
dim
=
self
.
dim
,
).
scan
# 2. create a second level of indirection for dark and flat and check
...
...
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