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tomotools
nxtomomill
Commits
aa11e808
Commit
aa11e808
authored
Jan 11, 2022
by
Henri Payno
Browse files
PEP8
parent
e4cf2f9f
Pipeline
#64515
passed with stages
in 6 minutes and 21 seconds
Changes
26
Pipelines
3
Hide whitespace changes
Inline
Side-by-side
nxtomomill/__main__.py
View file @
aa11e808
...
...
@@ -36,15 +36,14 @@ __date__ = "04/01/2018"
import
logging
logging
.
basicConfig
()
import
sys
from
silx.utils.launcher
import
Launcher
as
_Launcher
import
nxtomomill.version
from
collections
import
namedtuple
import
traceback
logging
.
basicConfig
()
DeprecationWarning
=
namedtuple
(
"DeprecationWarning"
,
[
"since"
,
"reason"
,
"replacement"
]
...
...
nxtomomill/app/test/test_dxfile2nx_app.py
View file @
aa11e808
...
...
@@ -38,7 +38,6 @@ import tempfile
from
nxtomomill.test.utils.dxfile
import
MockDxFile
from
nxtomomill.app.dxfile2nx
import
main
import
os
import
subprocess
def
test_dxfile2nx_application
():
...
...
@@ -50,7 +49,7 @@ def test_dxfile2nx_application():
n_darks
=
2
n_flats
=
4
mock
=
MockDxFile
(
MockDxFile
(
file_path
=
dx_file_path
,
n_projection
=
n_projections
,
n_darks
=
n_darks
,
...
...
nxtomomill/app/test/test_edf2nx_app.py
View file @
aa11e808
...
...
@@ -38,7 +38,6 @@ import tempfile
from
tomoscan.esrf.mock
import
MockEDF
from
nxtomomill.app.edf2nx
import
main
import
os
import
subprocess
def
test_edf2nx_application
():
...
...
nxtomomill/app/test/test_h52nx_app.py
View file @
aa11e808
...
...
@@ -38,7 +38,6 @@ import tempfile
from
nxtomomill.test.utils.bliss
import
MockBlissAcquisition
from
nxtomomill.app.h52nx
import
main
import
os
import
subprocess
def
test_h52nx_application
():
...
...
nxtomomill/app/test/test_patch_nx_app.py
View file @
aa11e808
...
...
@@ -37,9 +37,7 @@ __date__ = "30/08/2021"
import
tempfile
from
tomoscan.esrf.mock
import
MockHDF5
from
nxtomomill.app.patch_nx
import
main
import
h5py
import
os
import
subprocess
def
test_patch_nx_application
():
...
...
nxtomomill/converter/__init__.py
View file @
aa11e808
from
.edf.edfconverter
import
edf_to_nx
from
.hdf5.hdf5converter
import
from_h5_to_nx
from
.hdf5.hdf5converter
import
h5_to_nx
from
.hdf5.hdf5converter
import
get_bliss_tomo_entries
from
.edf.edfconverter
import
EDFFileKeys
from
.dxfile.dxfileconverter
import
from_dx_to_nx
from
.edf.edfconverter
import
edf_to_nx
# noqa F401
from
.hdf5.hdf5converter
import
from_h5_to_nx
# noqa F401
from
.hdf5.hdf5converter
import
h5_to_nx
# noqa F401
from
.hdf5.hdf5converter
import
get_bliss_tomo_entries
# noqa F401
from
.edf.edfconverter
import
EDFFileKeys
# noqa F401
from
.dxfile.dxfileconverter
import
from_dx_to_nx
# noqa F401
nxtomomill/converter/dxfile/__init__.py
View file @
aa11e808
...
...
@@ -31,4 +31,4 @@ __authors__ = ["H. Payno"]
__date__
=
"07/06/2020"
__license__
=
"MIT"
from
.dxfileconverter
import
from_dx_to_nx
from
.dxfileconverter
import
from_dx_to_nx
# noqa F401
nxtomomill/converter/dxfile/dxfileconverter.py
View file @
aa11e808
...
...
@@ -329,7 +329,7 @@ class _DxFileToNxConverter(BaseConverter):
if
self
.
energy
is
None
:
try
:
self
.
_configuration
.
energy
=
self
.
_read_energy
()
except
Exception
as
e
:
except
Exception
:
self
.
_configuration
.
energy
=
None
if
self
.
energy
is
None
:
self
.
_configuration
.
energy
=
self
.
DEFAULT_BEAM_ENERGY
...
...
@@ -552,7 +552,7 @@ class _DxFileToNxConverter(BaseConverter):
where
=
"end"
,
logger
=
_logger
,
).
process
()
except
Exception
as
e
:
except
Exception
:
_logger
.
warning
(
"No projections found in {} or unable to add them to the dataset"
.
format
(
self
.
_data_proj_url
.
path
()
...
...
nxtomomill/converter/edf/edfconverter.py
View file @
aa11e808
...
...
@@ -46,10 +46,10 @@ from nxtomomill.settings import Tomo
from
tomoscan.esrf.edfscan
import
EDFTomoScan
from
tomoscan.unitsystem
import
metricsystem
from
tomoscan.io
import
HDF5File
import
datetime
import
fabio
import
numpy
import
os
import
logging
EDF_MOTOR_POS
=
Tomo
.
EDF
.
MOTOR_POS
EDF_MOTOR_MNE
=
Tomo
.
EDF
.
MOTOR_MNE
...
...
@@ -61,8 +61,6 @@ EDF_X_TRANS = Tomo.EDF.X_TRANS
EDF_Y_TRANS
=
Tomo
.
EDF
.
Y_TRANS
EDF_Z_TRANS
=
Tomo
.
EDF
.
Z_TRANS
import
logging
_logger
=
logging
.
getLogger
(
__name__
)
...
...
@@ -181,7 +179,7 @@ def edf_to_nx(
.
split
(
" "
)
.
index
(
file_keys
.
rot_angle_key
)
)
except
:
except
(
KeyError
,
ValueError
)
:
rotangle_index
=
-
1
try
:
xtrans_index
=
(
...
...
@@ -189,7 +187,7 @@ def edf_to_nx(
.
split
(
" "
)
.
index
(
file_keys
.
x_trans_key
)
)
except
:
except
(
KeyError
,
ValueError
)
:
xtrans_index
=
-
1
try
:
ytrans_index
=
(
...
...
@@ -197,7 +195,7 @@ def edf_to_nx(
.
split
(
" "
)
.
index
(
file_keys
.
y_trans_key
)
)
except
:
except
(
KeyError
,
ValueError
)
:
ytrans_index
=
-
1
try
:
ztrans_index
=
(
...
...
@@ -205,7 +203,7 @@ def edf_to_nx(
.
split
(
" "
)
.
index
(
file_keys
.
z_trans_key
)
)
except
:
except
(
KeyError
,
ValueError
)
:
ztrans_index
=
-
1
if
hasattr
(
fid
,
"bytecode"
):
...
...
@@ -248,7 +246,7 @@ def edf_to_nx(
if
sample_name
is
None
:
try
:
sample_name
=
os
.
path
.
abspath
(
scan
.
path
).
split
(
os
.
sep
)[
-
3
:]
except
:
except
Exception
:
sample_name
=
"unknow"
h5d
[
"/entry/sample/name"
]
=
sample_name
if
instrument_name
is
not
None
:
...
...
@@ -363,7 +361,7 @@ def edf_to_nx(
else
:
data
=
fabio_file
.
getframe
(
index
).
data
header
=
fabio_file
.
getframe
(
index
).
header
except
Exception
as
e
:
except
Exception
:
data
=
None
header
=
None
finally
:
...
...
@@ -614,7 +612,7 @@ def edf_to_nx(
# create beam group at root for compatibility
try
:
link_nxbeam_to_root
(
file_path
=
output_file
,
entry_path
=
"entry"
)
except
Exception
as
e
:
except
Exception
:
pass
return
fileout_h5
,
"entry"
nxtomomill/converter/edf/test/test_edf2nx.py
View file @
aa11e808
...
...
@@ -28,7 +28,6 @@ __license__ = "MIT"
__date__
=
"09/10/2020"
import
shutil
import
tempfile
import
os
from
nxtomomill
import
converter
...
...
@@ -52,7 +51,7 @@ def test_edf_to_nx_converter(progress):
n_proj
=
120
n_alignment_proj
=
5
dim
=
100
mock
=
MockEDF
(
MockEDF
(
scan_path
=
scan_path
,
n_radio
=
n_proj
,
n_ini_radio
=
n_proj
,
...
...
nxtomomill/converter/hdf5/acquisition/baseacquisition.py
View file @
aa11e808
...
...
@@ -36,7 +36,7 @@ __date__ = "27/11/2020"
import
h5py
try
:
import
hdf5plugin
import
hdf5plugin
# noqa F401
except
ImportError
:
pass
from
nxtomomill.plugins
import
(
...
...
@@ -525,7 +525,7 @@ class BaseAcquisition:
info_retrieve
=
resource_name
,
expected_unit
=
None
,
)
except
(
ValueError
,
KeyError
)
as
e
:
except
(
ValueError
,
KeyError
):
pass
else
:
return
values
,
None
...
...
nxtomomill/converter/hdf5/acquisition/standardacquisition.py
View file @
aa11e808
...
...
@@ -52,7 +52,7 @@ from silx.io.url import DataUrl
from
typing
import
Union
try
:
import
hdf5plugin
import
hdf5plugin
# noqa F401
except
ImportError
:
pass
import
logging
...
...
nxtomomill/converter/hdf5/acquisition/utils.py
View file @
aa11e808
...
...
@@ -37,7 +37,7 @@ import typing
import
h5py
try
:
import
hdf5plugin
import
hdf5plugin
# noqa F401
except
ImportError
:
pass
import
logging
...
...
@@ -84,7 +84,7 @@ def get_entry_type(
try
:
title
=
h5py_read_dataset
(
entry
[
"title"
])
except
Exception
as
e
:
except
Exception
:
_logger
.
error
(
"fail to find title for %s, skip this group"
%
entry
.
name
)
else
:
init_titles
=
list
(
configuration
.
init_titles
)
...
...
nxtomomill/converter/hdf5/acquisition/xrdctacquisition.py
View file @
aa11e808
...
...
@@ -42,7 +42,7 @@ import h5py
from
silx.io.url
import
DataUrl
try
:
import
hdf5plugin
import
hdf5plugin
# noqa F401
except
ImportError
:
pass
import
logging
...
...
@@ -137,4 +137,4 @@ class XRDCTAcquisition(StandardAcquisition):
def
_write_beam
(
self
,
root_node
,
request_input
,
input_callback
):
instrument_node
=
root_node
.
require_group
(
"instrument"
)
beam_node
=
instrument_node
.
require_group
(
"beam"
)
instrument_node
.
require_group
(
"beam"
)
nxtomomill/converter/hdf5/acquisition/zseriesacquisition.py
View file @
aa11e808
...
...
@@ -46,7 +46,7 @@ import h5py
from
silx.io.url
import
DataUrl
try
:
import
hdf5plugin
import
hdf5plugin
# noqa F401
except
ImportError
:
pass
...
...
@@ -59,7 +59,7 @@ def is_z_series_frm_titles(entry: h5py.Group, configuration: TomoHDF5Config) ->
"""
try
:
title
=
h5py_read_dataset
(
entry
[
"title"
])
except
Exception
as
e
:
except
Exception
:
return
False
else
:
return
title
in
configuration
.
zserie_init_titles
...
...
nxtomomill/converter/hdf5/hdf5converter.py
View file @
aa11e808
...
...
@@ -60,10 +60,10 @@ import os
import
h5py
try
:
import
hdf5plugin
import
hdf5plugin
# noqa F401
except
ImportError
:
pass
#
# import that should be removed when h5_to_nx will be removed
# import that should be removed when h5_to_nx will be removed
from
nxtomomill.converter.hdf5.utils
import
H5FileKeys
from
nxtomomill.converter.hdf5.utils
import
H5ScanTitles
...
...
nxtomomill/io/__init__.py
View file @
aa11e808
from
.config
import
*
from
.config
import
*
# noqa F401,F403
nxtomomill/io/config.py
View file @
aa11e808
...
...
@@ -22,7 +22,7 @@
# THE SOFTWARE.
#
#
# ###########################################################################
*/
# ###########################################################################
"""
contains the HDF5Config
...
...
@@ -1099,7 +1099,7 @@ class TomoHDF5Config:
]
flat_titles_dks
.
extend
(
TomoHDF5Config
.
FLAT_TILES_ALIASES
)
flat_title_key_picked
=
None
#
#
handle flat titles
# handle flat titles
for
alias
in
flat_titles_dks
:
flat_titles
=
dict_
.
get
(
alias
,
None
)
if
flat_titles
is
not
None
:
...
...
nxtomomill/io/framegroup.py
View file @
aa11e808
...
...
@@ -107,8 +107,6 @@ class FrameGroup:
@
url
.
setter
def
url
(
self
,
url
:
Union
[
DataUrl
,
str
]):
if
isinstance
(
url
,
str
):
from
nxtomomill.io.utils
import
is_url_path
# handle if the string path is not a "full url" then we consider
# this is only the data path.
self
.
_url
=
DataUrl
(
path
=
url
)
...
...
@@ -200,7 +198,7 @@ class FrameGroup:
urls_str
=
",
\n
"
.
join
([
"{}"
.
format
(
str
(
url
))
for
url
in
urls
])
return
"""(
{}
)
)
"""
.
format
(
urls_str
)
...
...
@@ -211,7 +209,7 @@ class FrameGroup:
Create an instance of FrameGroup from it string representation.
"""
if
not
isinstance
(
input_str
,
str
):
raise
TypeError
(
"
input_str should be a string"
.
format
(
input_str
)
)
raise
TypeError
(
f
"
{
input_str
}
should be a string"
)
from
nxtomomill.io.utils
import
(
remove_parenthesis_or_brackets
,
...
...
@@ -333,7 +331,7 @@ def filter_acqui_frame_type(
frame_types
=
frame_types
[
current_acqui_idx
+
1
:]
try
:
next_acqui
=
frame_types
.
index
(
AcquisitionStep
.
INITIALIZATION
)
-
1
except
ValueError
as
e
:
except
ValueError
:
next_acqui
=
-
1
sequence_target
=
sequence_target
[:
next_acqui
]
filter_fct
=
lambda
a
:
a
.
frame_type
is
frame_type
...
...
nxtomomill/io/test/test_config.py
View file @
aa11e808
...
...
@@ -31,7 +31,7 @@ __date__ = "23/02/2021"
import
unittest
import
shutil
import
tempfile
from
nxtomomill.io.config
import
TomoHDF5Config
,
generate_default_h5_config
from
nxtomomill.io.config
import
TomoHDF5Config
from
nxtomomill
import
settings
import
os
...
...
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