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1013: NeXus Loading Window #1024

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Jun 28, 2021
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b1165a1
new files
DolicaAkelloEgwel Jun 7, 2021
0f6fc9d
window appearing
DolicaAkelloEgwel Jun 8, 2021
cf6dd85
adding items to list
DolicaAkelloEgwel Jun 8, 2021
9b39363
pixel size and bit depth
DolicaAkelloEgwel Jun 8, 2021
dd4979a
widget names
DolicaAkelloEgwel Jun 8, 2021
003ab98
choose nexus file and change line edit
DolicaAkelloEgwel Jun 8, 2021
ff2e9ac
moving nexus loader methods
DolicaAkelloEgwel Jun 10, 2021
5abc5d1
Merge branch 'master' into 1013_nexus_loading_window
DolicaAkelloEgwel Jun 10, 2021
bb21ea2
updating when image key is found
DolicaAkelloEgwel Jun 10, 2021
b188e1b
data tree
DolicaAkelloEgwel Jun 10, 2021
1e87244
flat/dark before/after
DolicaAkelloEgwel Jun 10, 2021
e19e8cd
not used at the moment
DolicaAkelloEgwel Jun 10, 2021
30e6b66
better column sizing
DolicaAkelloEgwel Jun 10, 2021
3557b17
baggage not needed
DolicaAkelloEgwel Jun 11, 2021
7b373f9
fixing paths
DolicaAkelloEgwel Jun 11, 2021
4666612
array sizes
DolicaAkelloEgwel Jun 11, 2021
bc7b19f
Merge branch 'master' into 1013_nexus_loading_window
DolicaAkelloEgwel Jun 11, 2021
db42ded
helper methods
DolicaAkelloEgwel Jun 11, 2021
c81d5c8
can't not use projections
DolicaAkelloEgwel Jun 14, 2021
d6631f1
empty invalid file opened method
DolicaAkelloEgwel Jun 14, 2021
52e25b4
just using get_images for flat/dark arrays
DolicaAkelloEgwel Jun 14, 2021
864208c
using set text rather than label like a baka
DolicaAkelloEgwel Jun 14, 2021
5a92b99
some constants
DolicaAkelloEgwel Jun 14, 2021
7368fd4
renaming methods
DolicaAkelloEgwel Jun 14, 2021
4eee557
Merge branch 'master' into 1013_nexus_loading_window
DolicaAkelloEgwel Jun 14, 2021
c00708a
set found status method
DolicaAkelloEgwel Jun 15, 2021
7ebd6b3
changing state of OK button
DolicaAkelloEgwel Jun 15, 2021
73b307f
remove repeat log message
DolicaAkelloEgwel Jun 15, 2021
72fb5bb
Merge branch 'master' into 1013_nexus_loading_window
DolicaAkelloEgwel Jun 15, 2021
47e1b65
clearing columns when file is chosen
DolicaAkelloEgwel Jun 15, 2021
a6f283c
resetting tree
DolicaAkelloEgwel Jun 15, 2021
9aa6c13
makes no difference
DolicaAkelloEgwel Jun 15, 2021
18224f4
making a dataset
DolicaAkelloEgwel Jun 15, 2021
b687d27
connecting checkboxes
DolicaAkelloEgwel Jun 15, 2021
58bbd4d
wrong arguments
DolicaAkelloEgwel Jun 15, 2021
d4329fb
docstrings in presenter
DolicaAkelloEgwel Jun 16, 2021
21798bd
retrieving title before file is closed
DolicaAkelloEgwel Jun 16, 2021
4dc7f34
docstrings for view
DolicaAkelloEgwel Jun 16, 2021
154a34a
Missing data and exception functions for view
DolicaAkelloEgwel Jun 16, 2021
8402e06
Tidy
DolicaAkelloEgwel Jun 16, 2021
08f6185
using pixel bit dpeth
DolicaAkelloEgwel Jun 16, 2021
21e4cb8
removing old nexus loader
DolicaAkelloEgwel Jun 16, 2021
e7ea335
solution for mypy error
DolicaAkelloEgwel Jun 16, 2021
aae8006
using pixel size information
DolicaAkelloEgwel Jun 16, 2021
4b4408a
superfluous argument
DolicaAkelloEgwel Jun 16, 2021
c27193d
tidy
DolicaAkelloEgwel Jun 16, 2021
69ae1cf
trying to fix tests
DolicaAkelloEgwel Jun 16, 2021
9dd44bd
return when data is missing
DolicaAkelloEgwel Jun 16, 2021
01985b2
test fixes
DolicaAkelloEgwel Jun 17, 2021
6a9d8f2
look for image key last
DolicaAkelloEgwel Jun 17, 2021
f0023fe
unable to find required fields tests
DolicaAkelloEgwel Jun 17, 2021
68f3006
open nexus file using path from view test
DolicaAkelloEgwel Jun 17, 2021
1faef3f
converting pixel size to int
DolicaAkelloEgwel Jun 17, 2021
424d689
test for get_dataset return
DolicaAkelloEgwel Jun 17, 2021
146bbdc
test file passing
DolicaAkelloEgwel Jun 17, 2021
e39088a
copyright
DolicaAkelloEgwel Jun 17, 2021
abf9a33
tests for view changes
DolicaAkelloEgwel Jun 17, 2021
76d0230
array comparison test
DolicaAkelloEgwel Jun 17, 2021
6d56550
changing missing data string
DolicaAkelloEgwel Jun 17, 2021
10b12d4
missing data tests
DolicaAkelloEgwel Jun 17, 2021
2abcefe
checkbox tests
DolicaAkelloEgwel Jun 17, 2021
da70d5a
mypy
DolicaAkelloEgwel Jun 21, 2021
9b5426a
test
DolicaAkelloEgwel Jun 21, 2021
30125e9
isinstance doesn't accept h5py types
DolicaAkelloEgwel Jun 21, 2021
5f178d4
test fixes
DolicaAkelloEgwel Jun 21, 2021
819e749
checkbox ticked by default
DolicaAkelloEgwel Jun 21, 2021
ce55cc4
Merge branch 'master' into 1013_nexus_loading_window
DolicaAkelloEgwel Jun 23, 2021
5e61a95
trying out applitools test
DolicaAkelloEgwel Jun 23, 2021
8fc3211
wrong triggers
DolicaAkelloEgwel Jun 23, 2021
6e80ec9
typo
DolicaAkelloEgwel Jun 23, 2021
b682132
Fixing nexus filename
DolicaAkelloEgwel Jun 23, 2021
54701fa
nonexistent view
DolicaAkelloEgwel Jun 23, 2021
b7f9850
wrong method location
DolicaAkelloEgwel Jun 23, 2021
73e51de
using set text
DolicaAkelloEgwel Jun 23, 2021
fdb0f64
test for main window
DolicaAkelloEgwel Jun 23, 2021
cb79796
Test for execute nexus load
DolicaAkelloEgwel Jun 25, 2021
16f070b
Release notes
DolicaAkelloEgwel Jun 25, 2021
892d9a6
Image in docs
DolicaAkelloEgwel Jun 25, 2021
d570fa1
docs update
DolicaAkelloEgwel Jun 25, 2021
5d0578a
syntax fix
DolicaAkelloEgwel Jun 25, 2021
25571ed
tidy
DolicaAkelloEgwel Jun 25, 2021
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1 change: 1 addition & 0 deletions .github/workflows/conda.yml
Original file line number Diff line number Diff line change
Expand Up @@ -69,6 +69,7 @@ jobs:
GITHUB_BRANCH_NAME: ${{ github.head_ref }}
run: |
git clone https://github.com/mantidproject/mantidimaging-data.git ~/mantidimaging-data
wget -O ~/mantidimaging-data/24737.nxs https://github.com/DiamondLightSource/Savu/blob/master/test_data/data/24737.nxs?raw=true
xvfb-run --auto-servernum python -m pytest -p no:xdist -p no:randomly -p no:repeat -p no:cov mantidimaging/eyes_tests
timeout-minutes: 15

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1 change: 1 addition & 0 deletions docs/release_notes/next.rst
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Expand Up @@ -14,6 +14,7 @@ New features
- #964 : Open NeXus files
- #1010 : Write slope and offset into int tiffs
- #987 : Allow Flat-fielding without dark subtraction
- #1013 : NeXus Loading Window

Fixes
-----
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22 changes: 14 additions & 8 deletions docs/user_guide/gui/loading_saving.rst
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Expand Up @@ -51,13 +51,19 @@ prior to saving.
NeXus Files
-----------

NeXus Files can be loaded by selecting the "Load NeXus file" on the File menu. Once a file has been chosen, the program
will attempt to find projections, dark images, and flat images by using the information contained in the NeXus
:code:`image_key` field. If an :code:`image_key` is not found, then the program will assume all the images in the file
are projections.
NeXus Files can be loaded by selecting the "Load NeXus file" on the File menu. This brings up the NeXus Load dialog
shown below.

The name given to the file will be taken from the :code:`title` field in the NeXus file if one is found, otherwise the
images are given the name "NeXus Data."
.. image:: ../../_static/nexus_loading_window.png
:alt: NeXus Load Dialog

If the loading is successful, the new images should appear in the main view of Mantid Imaging. Information related to
issues encountered while loading the file will be displayed as log messages as well as appearing in a popup window.
From here you can choose a NeXus file that you wish to load. The program will then scan its contents and check for a
:code:`NXtomo` entry. If an entry is found, information about the file will be displayed in the dialog. The data sizes
are also displayed so that a user can check that the image key and data field have the same number of elements. The
"Use?" checkbox can be used to select which images you wish to load.

If the required information could be found in the file, then the OK button will be enabled. Otherwise the button will be
disabled.

From here, you can press OK to load the file as a dataset. The name given to the images will be taken from the
:code:`title` field in the NeXus file if one is found, otherwise the images are given the name "NeXus Data."
202 changes: 0 additions & 202 deletions mantidimaging/core/io/loader/nexus_loader.py

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