Design and create GUI for IMAT reconstruction

[John Hill]

Design and create a GUI for configuring, submitting and monitoring reconstruction jobs from the IMAT instrument.

The interface must also provide a mechanism for creating and loading hdf5 files containing the parameters, to save/restore options.

[John Hill]

(In #10766) Needs to be checked and updated when the file structure is finalised. Currently accepts a list of Table Workspaces which are written to a nexus file.

Each Table contains a single row with four columns:

• id - unique Plugin ID

• params - json string of name/value pairs for each parameter

• name - user friendly description of the plugin

• cite - citation information about the plugin author

[John Hill]

Refs #10564 adding files and first parameter editor implementation

Changeset: fbd2eca20ee2a5fd72fb136f505d54916366445f

[Federico Montesino Pouzols]

Compile on other platforms and fixes to compile, re #10564

Changeset: 2deb30dcb3a5f250b49d31001dbaacc04d8318a6

[Federico Montesino Pouzols]

use LoadTomoConfig alg, reduce dependencies, gui goodies, re #10564

Changeset: 80260d59905e65eff18afb3296a63526d685e92a

[Federico Montesino Pouzols]

OwnTree to cpp and documentation, re #10564

Changeset: 3651281ac4216a6b804a22eb1781a0f18141f5ee

[Federico Montesino Pouzols]

remove unnecessary headers, uuid missing on rhel6, re #10564

Changeset: 6dfc8299d4d2876d7fb258891d11fe83ed46fe74

[Federico Montesino Pouzols]

directly throw original except instead of copy, cppcheck, re #10564

Changeset: 7edb72f065b27fa8aa79561649f8830621bbdc6a

[Federico Montesino Pouzols]

fix cppcheck issue, prefer init list, re #10564

Changeset: cfdc5b0ba5db6f4cd25dba0b9208f507fc3f13b0

[Federico Montesino Pouzols]

pass string by ref, re #10564

Changeset: b6f7f5be7a59b153b87aa82d62be0ff494ff68a7

[Federico Montesino Pouzols]

put tomo files back into cmakelists after merge, re #10564

Changeset: 0556615104150b033a50cac72f512ce3dbff495d

[Federico Montesino Pouzols]

clang-format it, re #10564

Changeset: ffba2a38d529de298093183ee445fdacc02be5e6

[Federico Montesino Pouzols]

expand tabs and bring them up to date, re #10564

Changeset: 6f9bbadc69a985d9c7cabd22409ff3100dbb6504

[Federico Montesino Pouzols]

more gui stuff, job control chunks, re #10564

Changeset: ad76004fb8ed932384f07b623ffa502d44ab2ddc

[Federico Montesino Pouzols]

add names for several relevant widgets, re #10564

Changeset: fcae4c596e51f6209e9aea67d776524919757cdb

[Federico Montesino Pouzols]

Filling in more actions, checks for resource, re #10564

Changeset: 6e9243cd431a8a75cd65c7d1847678553113bc05

[Federico Montesino Pouzols]

added code for ping and query status actions, re #10564

Changeset: faefe05e32e745c6eb597b80e2e2d4ab5cad316a

[Federico Montesino Pouzols]

more compute resource, login/logout functionality, re #10564

Changeset: 7a5388cf29eda2934de9ca49007bc09ff959dd96

[Federico Montesino Pouzols]

build basic job command line, re #10564

Changeset: 28f38dd2a6ef7b0ed38737f02ae4fa1c3233fc35

[Federico Montesino Pouzols]

Merge branch 'master' into feature/10564_tomo_reconstruction_gui

Conflicts:

Code/Mantid/MantidQt/CustomInterfaces/CMakeLists.txt

Sort out easy conflict in custom interfaces cmakelists.

This merge brings in the SCARFTomoReconstruction algorithm and the Load/SaveSavuConfig algorithms, all required in the IMAT GUI.

Re #10564

Changeset: 42c0da81d114c1f8f82f400daa5db761f6cd8eb2

[Federico Montesino Pouzols]

paint and show fits images, and table (job info) refresh, re #10564

Changeset: 467d51af03f8927ca488b17963ba2e73f659734d

[Federico Montesino Pouzols]

get config paths from several browse buttons, re #10564

Changeset: ebce3ac4b6c5ef22a3c1cb25111edb50fb8ff66a

[Federico Montesino Pouzols]

added input property to set the job name, also astra jobs, re #10564

Changeset: 0cae2b197d35fc2674ca81bb702ac8b530a26f42

[Federico Montesino Pouzols]

use job paths, use only one tableWS for savu plugins list, re #10564

Changeset: 8aaa7b5e995c3c9d89371e455c760313a7768051

[Federico Montesino Pouzols]

update tab name, it's savu specific, re #10564

Changeset: 5a8e5a609cc6f4ce0183b0382647e9d8b810dfc3

[Federico Montesino Pouzols]

do a better job with list/array parameters, don't crash, re #10564

Changeset: 77645f50419f07984810719a19ec9e44c3320c72

[Federico Montesino Pouzols]

destructor logs out, re #10564

Changeset: 87c6a2fd9f13b2eb29fa7361b5543a8289c298f3

[Federico Montesino Pouzols]

reconstruct push tooltip, and basic tool options dialog, re #10564

Changeset: 9797a22d072086b4f3d9a63c913368e08daa3dc1

[Federico Montesino Pouzols]

move savu config tab out to its own window, re #10564

Changeset: a46f98f9e1e4b9116ef733ba794331a8c81d23e5

[Federico Montesino Pouzols]

added basic dialogs for tool specific config, re #10564

Changeset: 251e3f63954f6f97051da80a502cec9bcdd7dccb

[Federico Montesino Pouzols]

initial support for .tif images (also png), re #10564

Changeset: 9c6a368b452d3fc5c349dfb65b5a66eabdda5447

[Federico Montesino Pouzols]

remove remaining bits of savu in general setup, re #10564

Changeset: 204c2c3fc7dcaa579e73c5f47ddacb00cdb09616

[Federico Montesino Pouzols]

remove old savu widgets, re #10564

Changeset: c5a1b5e893c8556490a561722f30811ada896761

[Federico Montesino Pouzols]

more tomo related files into its own subdirectory, re #10564

Changeset: b1952640b7428f5b9c501bfcf6df51b030a93444

[Federico Montesino Pouzols]

update new paths to sources and headers, re #10564

Changeset: 7de24111fbf139b0261d054013e64ac309840534

[Federico Montesino Pouzols]

update tool setup interfaces with params, re #10564

Changeset: 7f0e96451884ff3ec30fc09a278d52ad9884b6db

[Federico Montesino Pouzols]

Merge remote-tracking branch 'origin/master' into feature/10564_tomo_reconstruction_gui

Conflicts:

Code/Mantid/MantidQt/CustomInterfaces/CMakeLists.txt

Keep all new files in this and other branches, re #10564

Changeset: 94204f62f8b4d6c2e64899d4735761f31e9d62ab

[Federico Montesino Pouzols]

This is being verified as ​pull request #544.

[Federico Montesino Pouzols]

fix misc issues caught by old compilers and cppcheck, re #10564

Changeset: 310f53d5cd0e717b99143221752e9e833b4cd994

[Federico Montesino Pouzols]

sort out conflict, recent changes to multidatasetfit, re #10564

Changeset: cecc954c65d85d3d5661d760839c417f6f8442fc

[Federico Montesino Pouzols]

kill old file left in cmake ui list after merge conflict, re #10564

Changeset: 45e6ab24b9be1da024e8c8dc038ae1c151618577

[Federico Montesino Pouzols]

start interface documentation as rst, re #10564

Changeset: 0fd717459611ce39f36a193cf418b79ebaa0a09f

[Federico Montesino Pouzols]

more on data formats and tools, re #10564

Changeset: 4a206c5200e3d9b51941822f9015d6250b8b2652

[Federico Montesino Pouzols]

help and cancel button, save/restore some settings, re #10564

Changeset: 8f5266a47fa9e227f1ebbfa12fa0ec01d7ffa4f6

[Federico Montesino Pouzols]

switch tabs, and put slots in their right place, re #10564

Changeset: ada1b5a26ee7145f82a952619d0abee54c25125d

[Federico Montesino Pouzols]

leave savu screenshot out for now, re #10564

Changeset: 36dd9674ecfb52be441f2f731279e3d00a318a12

[Federico Montesino Pouzols]

use on_ prefix for qt slot methods, re #10564

Changeset: 213b174f49e33400508a231169b057d164768447

[Federico Montesino Pouzols]

close window property, doc fixes and other minor things, re #10564

Changeset: e7332f00ec80e44cc4156d27cfac2b8239c78de5

[Ross Whitfield]

:fire: The most recent changes caused all the build servers to get stuck on

reading sources... [ 99%] interfaces/Tomographic_Reconstruction QObject::connect: Cannot connect QPushButton::released() to (null)::close()

and I had to manually kill the jobs. I think they were waiting for a user to press a button during exit but the build servers aren't sentient enough to realised that. Make sure your next commit fixes this else the build servers will get stuck again. :worried:

[Federico Montesino Pouzols]

Aha, thanks for fixing it. I guess that's why the queue was growing so wildly yesterday evening. I had no idea that this could happen. I'll make a temp fix for it.

[Federico Montesino Pouzols]

save prefs, default: don't ask user when closing, re #10564

Changeset: 89e4f4747b6bb2c3cf4a577daddd0b2d3e051424

[Federico Montesino Pouzols]

filling in missing doc sections, re #10564

Changeset: 465fd4a41810873f2075bb80ee953affc588fa22

[Federico Montesino Pouzols]

rearrange scarf login widgets, fix job kill, re #10564

Changeset: f34ae3281a25fef8255d56f41beedbfffdee7eef

[Federico Montesino Pouzols]

handle keep-alive and periodic job status update, re #10564

Changeset: 8fb11a6d47c79c6d7558c9455e21a587de8a2055

[Federico Montesino Pouzols]

fix accidentally modified ui, in prev commit, re #10564

Changeset: 12db3f38b178297aa4e77107e2cf9626b4ae6b67

[Federico Montesino Pouzols]

QThread -> QTimer, simpler, re #10564

Changeset: 0de3a486400f7f369b06ac5d45353233d50efe07

[Federico Montesino Pouzols]

start timer in a separate thread, re #10564

Changeset: 970730966b026ad6ab8e115c4a72ba8cce72847f

[Federico Montesino Pouzols]

polishing interface and documentation details, re #10564

Changeset: af22323825454c72daddf1a6af83726f9a474507

[Federico Montesino Pouzols]

tidy up settings and dialog classes a bit, re #10564

Changeset: 7f01136e2c303618260d029d0769054d1d476ee9

[Federico Montesino Pouzols]

explain more the setup tab, re #10564

Changeset: 9ee753e4eb695b891d8da27e69a8bd2194cfcf06

[Federico Montesino Pouzols]

fix doxygen warnings and cppcheck style warning, re #10564

Changeset: 9ecdb79cea40e71388478bbf139b25b8dd6819fa

[Federico Montesino Pouzols]

setup dialogs: fix crash and signals, also show savu setup, re #10564

Changeset: 2511ce212d7bd9757b259f2f7b205692163bd70f

[Federico Montesino Pouzols]

We found a crash in the Astra setup dialog, and also the TomoPy setup wasn't working well. It should be fixed now. This just emphasizes that tests should be added asap (#11193(​http://trac.mantidproject.org/mantid/ticket/11193)). To reproduce follow these steps:

• Go to 'Setup' and Log in (needs my username/password)
• Put something in the three 'base directories' in the 'Setup' tab
• Go to 'Run', select different tools, and do 'setup' before clicking on 'reconstruct'. Default values are ok for testing.
• Run jobs with them. All the tools available should behave now (with the exceptions noted below).

Notes:

• You should be able to submit TomoPy and 'Custom' jobs successfully (they should show up in the table of jobs).
• Astra is enabled in this custom interface but at the moment it won't work on SCARF. You should see a warning log message about this, and Astra jobs won't start. This might get fixed on SCARF soon.
• The savu setup dialog is enabled (I just changed this in the last commit), but savu is not yet available on SCARF. So in practice you cannot run jobs for savu (the dialog is enabled now so it can be shown to the IMAT scientists in our demos/chats) but you are not allowed to submit savu jobs.

• I've noticed that the cancel button doesn't work well at the moment. We get an error "Permission denied. Contact your administrator", this in principle is not a Mantid issue.

[Federico Montesino Pouzols]

g_ prefix for static members, and allow default output path, re #10564

Changeset: ab920bb5378a057ac935c148563166ac690e71a5

[Owen Arnold]

We've discussed the future direction of this interface, and I understand that a beta version is required now. The functionality we tried on it all worked. The code looks OK, but is lacking in separation and automated testing (another ticket for this). A wizard type approach would be better than the tab based system.

[John Hill]

Refs #10564 adding files and first parameter editor implementation

Changeset: fbd2eca20ee2a5fd72fb136f505d54916366445f

[Federico Montesino Pouzols]

Compile on other platforms and fixes to compile, re #10564

Changeset: 2deb30dcb3a5f250b49d31001dbaacc04d8318a6

[Federico Montesino Pouzols]

use LoadTomoConfig alg, reduce dependencies, gui goodies, re #10564

Changeset: 80260d59905e65eff18afb3296a63526d685e92a

[Federico Montesino Pouzols]

OwnTree to cpp and documentation, re #10564

Changeset: 3651281ac4216a6b804a22eb1781a0f18141f5ee

[Federico Montesino Pouzols]

remove unnecessary headers, uuid missing on rhel6, re #10564

Changeset: 6dfc8299d4d2876d7fb258891d11fe83ed46fe74

[Federico Montesino Pouzols]

fix cppcheck issue, prefer init list, re #10564

Changeset: cfdc5b0ba5db6f4cd25dba0b9208f507fc3f13b0

[Federico Montesino Pouzols]

pass string by ref, re #10564

Changeset: b6f7f5be7a59b153b87aa82d62be0ff494ff68a7

[Federico Montesino Pouzols]

put tomo files back into cmakelists after merge, re #10564

Changeset: 0556615104150b033a50cac72f512ce3dbff495d

[Federico Montesino Pouzols]

clang-format it, re #10564

Changeset: ffba2a38d529de298093183ee445fdacc02be5e6

[Federico Montesino Pouzols]

expand tabs and bring them up to date, re #10564

Changeset: 6f9bbadc69a985d9c7cabd22409ff3100dbb6504

[Federico Montesino Pouzols]

more gui stuff, job control chunks, re #10564

Changeset: ad76004fb8ed932384f07b623ffa502d44ab2ddc

[Federico Montesino Pouzols]

add names for several relevant widgets, re #10564

Changeset: fcae4c596e51f6209e9aea67d776524919757cdb

[Federico Montesino Pouzols]

Filling in more actions, checks for resource, re #10564

Changeset: 6e9243cd431a8a75cd65c7d1847678553113bc05

[Federico Montesino Pouzols]

added code for ping and query status actions, re #10564

Changeset: faefe05e32e745c6eb597b80e2e2d4ab5cad316a

[Federico Montesino Pouzols]

more compute resource, login/logout functionality, re #10564

Changeset: 7a5388cf29eda2934de9ca49007bc09ff959dd96

[Federico Montesino Pouzols]

build basic job command line, re #10564

Changeset: 28f38dd2a6ef7b0ed38737f02ae4fa1c3233fc35

[Federico Montesino Pouzols]

Merge branch 'master' into feature/10564_tomo_reconstruction_gui

Conflicts:

Code/Mantid/MantidQt/CustomInterfaces/CMakeLists.txt

Sort out easy conflict in custom interfaces cmakelists.

This merge brings in the SCARFTomoReconstruction algorithm and the Load/SaveSavuConfig algorithms, all required in the IMAT GUI.

Re #10564

Changeset: 42c0da81d114c1f8f82f400daa5db761f6cd8eb2

[Federico Montesino Pouzols]

paint and show fits images, and table (job info) refresh, re #10564

Changeset: 467d51af03f8927ca488b17963ba2e73f659734d

[Federico Montesino Pouzols]

get config paths from several browse buttons, re #10564

Changeset: ebce3ac4b6c5ef22a3c1cb25111edb50fb8ff66a

[Federico Montesino Pouzols]

added input property to set the job name, also astra jobs, re #10564

Changeset: 0cae2b197d35fc2674ca81bb702ac8b530a26f42

[Federico Montesino Pouzols]

use job paths, use only one tableWS for savu plugins list, re #10564

Changeset: 8aaa7b5e995c3c9d89371e455c760313a7768051

[Federico Montesino Pouzols]

update tab name, it's savu specific, re #10564

Changeset: 5a8e5a609cc6f4ce0183b0382647e9d8b810dfc3

[Federico Montesino Pouzols]

do a better job with list/array parameters, don't crash, re #10564

Changeset: 77645f50419f07984810719a19ec9e44c3320c72

[Federico Montesino Pouzols]

destructor logs out, re #10564

Changeset: 87c6a2fd9f13b2eb29fa7361b5543a8289c298f3

[Federico Montesino Pouzols]

reconstruct push tooltip, and basic tool options dialog, re #10564

Changeset: 9797a22d072086b4f3d9a63c913368e08daa3dc1

[Federico Montesino Pouzols]

move savu config tab out to its own window, re #10564

Changeset: a46f98f9e1e4b9116ef733ba794331a8c81d23e5

[Federico Montesino Pouzols]

added basic dialogs for tool specific config, re #10564

Changeset: 251e3f63954f6f97051da80a502cec9bcdd7dccb

[Federico Montesino Pouzols]

initial support for .tif images (also png), re #10564

Changeset: 9c6a368b452d3fc5c349dfb65b5a66eabdda5447

[Federico Montesino Pouzols]

remove remaining bits of savu in general setup, re #10564

Changeset: 204c2c3fc7dcaa579e73c5f47ddacb00cdb09616

[Federico Montesino Pouzols]

remove old savu widgets, re #10564

Changeset: c5a1b5e893c8556490a561722f30811ada896761

[Federico Montesino Pouzols]

more tomo related files into its own subdirectory, re #10564

Changeset: b1952640b7428f5b9c501bfcf6df51b030a93444

[Federico Montesino Pouzols]

update new paths to sources and headers, re #10564

Changeset: 7de24111fbf139b0261d054013e64ac309840534

[Federico Montesino Pouzols]

update tool setup interfaces with params, re #10564

Changeset: 7f0e96451884ff3ec30fc09a278d52ad9884b6db

[Federico Montesino Pouzols]

Merge remote-tracking branch 'origin/master' into feature/10564_tomo_reconstruction_gui

Conflicts:

Code/Mantid/MantidQt/CustomInterfaces/CMakeLists.txt

Keep all new files in this and other branches, re #10564

Changeset: 94204f62f8b4d6c2e64899d4735761f31e9d62ab

[Federico Montesino Pouzols]

fix misc issues caught by old compilers and cppcheck, re #10564

Changeset: 310f53d5cd0e717b99143221752e9e833b4cd994

[Federico Montesino Pouzols]

sort out conflict, recent changes to multidatasetfit, re #10564

Changeset: cecc954c65d85d3d5661d760839c417f6f8442fc

[Federico Montesino Pouzols]

kill old file left in cmake ui list after merge conflict, re #10564

Changeset: 45e6ab24b9be1da024e8c8dc038ae1c151618577

[Federico Montesino Pouzols]

start interface documentation as rst, re #10564

Changeset: 0fd717459611ce39f36a193cf418b79ebaa0a09f

[Federico Montesino Pouzols]

more on data formats and tools, re #10564

Changeset: 4a206c5200e3d9b51941822f9015d6250b8b2652

[Federico Montesino Pouzols]

help and cancel button, save/restore some settings, re #10564

Changeset: 8f5266a47fa9e227f1ebbfa12fa0ec01d7ffa4f6

[Federico Montesino Pouzols]

switch tabs, and put slots in their right place, re #10564

Changeset: ada1b5a26ee7145f82a952619d0abee54c25125d

[Federico Montesino Pouzols]

leave savu screenshot out for now, re #10564

Changeset: 36dd9674ecfb52be441f2f731279e3d00a318a12

[Federico Montesino Pouzols]

use on_ prefix for qt slot methods, re #10564

Changeset: 213b174f49e33400508a231169b057d164768447

[Federico Montesino Pouzols]

close window property, doc fixes and other minor things, re #10564

Changeset: e7332f00ec80e44cc4156d27cfac2b8239c78de5

[Federico Montesino Pouzols]

save prefs, default: don't ask user when closing, re #10564

Changeset: 89e4f4747b6bb2c3cf4a577daddd0b2d3e051424

[Federico Montesino Pouzols]

filling in missing doc sections, re #10564

Changeset: 465fd4a41810873f2075bb80ee953affc588fa22

[Federico Montesino Pouzols]

rearrange scarf login widgets, fix job kill, re #10564

Changeset: f34ae3281a25fef8255d56f41beedbfffdee7eef

[Federico Montesino Pouzols]

handle keep-alive and periodic job status update, re #10564

Changeset: 8fb11a6d47c79c6d7558c9455e21a587de8a2055

[Federico Montesino Pouzols]

fix accidentally modified ui, in prev commit, re #10564

Changeset: 12db3f38b178297aa4e77107e2cf9626b4ae6b67

[Federico Montesino Pouzols]

QThread -> QTimer, simpler, re #10564

Changeset: 0de3a486400f7f369b06ac5d45353233d50efe07

[Federico Montesino Pouzols]

start timer in a separate thread, re #10564

Changeset: 970730966b026ad6ab8e115c4a72ba8cce72847f

[Federico Montesino Pouzols]

polishing interface and documentation details, re #10564

Changeset: af22323825454c72daddf1a6af83726f9a474507

[Federico Montesino Pouzols]

tidy up settings and dialog classes a bit, re #10564

Changeset: 7f01136e2c303618260d029d0769054d1d476ee9

[Federico Montesino Pouzols]

explain more the setup tab, re #10564

Changeset: 9ee753e4eb695b891d8da27e69a8bd2194cfcf06

[Federico Montesino Pouzols]

fix doxygen warnings and cppcheck style warning, re #10564

Changeset: 9ecdb79cea40e71388478bbf139b25b8dd6819fa

[Federico Montesino Pouzols]

setup dialogs: fix crash and signals, also show savu setup, re #10564

Changeset: 2511ce212d7bd9757b259f2f7b205692163bd70f

[Federico Montesino Pouzols]

g_ prefix for static members, and allow default output path, re #10564

Changeset: ab920bb5378a057ac935c148563166ac690e71a5

[Owen Arnold]

Merge pull request #544 from mantidproject/feature/10564_tomo_reconstruction_gui

Add custom interface: tomographic reconstruction for IMAT

Full changeset: ​0d0a78839f81f68f06f362b6980bf93f349efc9c

[Stuart Campbell]

This ticket has been transferred to github issue ​11406