Ticket #5421 (closed: fixed)

Opened 8 years ago

Last modified 5 years ago

[IDA] Bayes - Implement New Interface

Reported by: Peter Parker Owned by: Samuel Jackson
Priority: major Milestone: Release 3.0
Component: Indirect Inelastic Keywords: IDA
Cc: spencer.howells@… Blocked By: #7926, #7964, #7965, #7966
Blocking: Tester: Peter Parker

Description

Following on from some of the files added as part of #5172, integrate Bayes functionality into an extra tab for the IDA interface.

Change History

comment:1 Changed 8 years ago by Peter Parker

Refs #5421 - Change from Spencer.

Changeset: e091b28d0a4e536fb5798081dd6b87754d168a52

comment:2 Changed 8 years ago by Peter Parker

Refs #5421 - Change from Spencer.

Changeset: e091b28d0a4e536fb5798081dd6b87754d168a52

comment:3 Changed 8 years ago by Peter Parker

Refs #5421 - Change from Spencer.

Changeset: e091b28d0a4e536fb5798081dd6b87754d168a52

comment:4 Changed 8 years ago by Nick Draper

  • Milestone changed from Release 2.2 to Release 2.3

Moved at the end of release 2.2

comment:5 Changed 8 years ago by Peter Parker

Update:

This is an ongoing ticket. The Bayes functionality is currently bundled along with Mantid via several algorithms in the Workflow->MIDAS category so that it may be tested by users before being implemented as a tab(s).

The relevant files here include:

  • Mantid/scripts/Inelastic/IndirectBayes.py, which contains most of the base code.

as well as the following PythonAlgorithms:

  • Mantid/Framework/PythonAPI/PythonAlgorithms/ResNorm.py
  • Mantid/Framework/PythonAPI/PythonAlgorithms/Quest.py
  • Mantid/Framework/PythonAPI/PythonAlgorithms/QLines.py
  • Mantid/Framework/PythonAPI/PythonAlgorithms/ILLines.py

To proceed we need more feedback from Spencer (and the users), as well as clarification about what the final tab should look like and what functionality should be on offer.

comment:6 Changed 8 years ago by Peter Parker

  • Keywords IDA added

comment:7 Changed 8 years ago by Nick Draper

  • Milestone changed from Release 2.3 to Release 2.4

Moved to milestone 2.4

comment:8 Changed 8 years ago by Dereck Kachere

  • Owner changed from Peter Parker to Dereck Kachere
  • Status changed from new to assigned

comment:9 Changed 8 years ago by Dereck Kachere

  • Milestone changed from Release 2.4 to Release 2.5

comment:10 Changed 7 years ago by Dereck Kachere

  • Cc spencer.howells@… added

comment:11 Changed 7 years ago by Nick Draper

  • Milestone changed from Release 2.5 to Release 2.6

Moved to r2.6 at the end of r2.5

comment:12 Changed 7 years ago by Nick Draper

  • Status changed from assigned to new

comment:13 Changed 7 years ago by Nick Draper

  • Component changed from Mantid to Framework

comment:14 Changed 7 years ago by Nick Draper

  • Milestone changed from Release 2.6 to Backlog

Moved to backlog at the code freeze for R2.6

comment:15 Changed 7 years ago by Samuel Jackson

  • Owner changed from Dereck Kachere to Samuel Jackson

comment:16 Changed 7 years ago by Samuel Jackson

  • Component changed from Framework to Indirect Inelastic

comment:17 Changed 7 years ago by Samuel Jackson

  • Milestone changed from Backlog to Release 3.0

comment:18 Changed 7 years ago by Samuel Jackson

  • Status changed from new to inprogress

Refs #5421 Adding skeleton code for Indirect Bayes.

Changeset: b96976c19d15afd477c166b84ea0257c13f7c6f4

comment:19 Changed 7 years ago by Samuel Jackson

Created Indirect Bayes window and ResNorm tab.

This commit also lays most of the ground work for the rest of the tabs.

Refs #5421

Changeset: e966be91df05b27d09b25ca8b51899a6c87fc1fc

comment:20 Changed 7 years ago by Samuel Jackson

Refs #5421 Adding interface for Quasi.

Changeset: 0c5a3acc6308fefc0bdf2800731359fb5b5cd7f7

comment:21 Changed 7 years ago by Samuel Jackson

Refs #5421 Adding Stretch interface.

Changeset: 1b077dcb3a074a6bd173d6d2c891a96e39d4feb8

comment:22 Changed 7 years ago by Samuel Jackson

Refs #5421 Created JumpFit interface.

Also refactored tabs to remove duplicate members.

Changeset: 5b821f1a9f278155ee30f9d2fa0a93770749e312

comment:23 Changed 7 years ago by Samuel Jackson

Refs #5421 Minor tweaks across the Bayes interface.

Changeset: 0cd930d19e59443d1bf9730b0f1f8fe4b1f3f549

comment:24 Changed 7 years ago by Samuel Jackson

  • Summary changed from [IDA] Bayes - Implement New Tab to [IDA] Bayes - Implement New Interface

comment:25 Changed 7 years ago by Samuel Jackson

  • Blocked By 7926 added

comment:26 Changed 7 years ago by Samuel Jackson

Refs #5421 Updates to Indirect Bayes for QLines.

Changeset: 174bbaa71f2bd725264825f251a48fc10380e18a

comment:27 Changed 7 years ago by Samuel Jackson

Refs #5421 Hooked up ResNorm to underlying python script.

This includes setting up the supporting code for the rest of the Bayes interface.

Changeset: 842879d30b8ae091fd27ba6a62078f83fdc81a8e

comment:28 Changed 7 years ago by Samuel Jackson

Refs #5421 Adding proper file filtering for ResNorm.

Changeset: 3009298cc6355fe08953f3d51a0343537b724976

comment:29 Changed 7 years ago by Samuel Jackson

Refs #5421 Added support for showing a message box to user.

Also properly documented the ResNorm code.

Changeset: 6e761905c8a5ff190d17a2190616b59eaf411921

comment:30 Changed 7 years ago by Samuel Jackson

Refs #5421 Added plotting of energy range and validation for it.

Changeset: 2e0eb51d03aed6e8c004ed81007c29992529b305

comment:31 Changed 7 years ago by Samuel Jackson

Refs #5421 More documentation and refactoring.

Changeset: 63542535a10f41c8609e3e4f036ee7e3da3caa4f

comment:32 Changed 7 years ago by Samuel Jackson

Refs #5421 Further refactoring.

Changeset: 8d00c24c0ea6a1902fb3dfcba294c9199abcb2cf

comment:33 Changed 7 years ago by Samuel Jackson

Refs #5421 Starting Quasi implementation.

Changeset: 444dbbda7b7ab1b1252b7fed2c83c2505efffd63

comment:34 Changed 7 years ago by Samuel Jackson

Refs #5421 Linked Quasi GUI code with python script.

Changeset: 9d8570e9dee547a64a3edb9b15b4f9e65346dc16

comment:35 Changed 7 years ago by Samuel Jackson

Refs #5421 Stretch interface now connected to Quest routine.

Changeset: fb774d9f846bd5d5c9c5b987c1cb4e0294b50e47

comment:36 Changed 7 years ago by Samuel Jackson

  • Blocked By 7964 added

comment:37 Changed 7 years ago by Samuel Jackson

  • Blocked By 7965 added

comment:38 Changed 7 years ago by Samuel Jackson

  • Blocked By 7966 added

comment:39 Changed 7 years ago by Samuel Jackson

Refs #5421 Minor tweaks to get the GUI working with the scripts.

Changeset: ec24e65b3bea816fca64beb68e048d7434173b55

comment:40 Changed 7 years ago by Samuel Jackson

Refs #5421 Merge branch 'feature/5421_IDA_bayes_interface' into

develop

Conflicts:

Code/Mantid/scripts/Inelastic/IndirectBayes.py

Changeset: 9b1a1c94f78ec88a4ec3c448c3a98cbe571f4f84

comment:41 Changed 7 years ago by Samuel Jackson

Refs #5421 Setting upper limits for Sigma/Beta in Stretch.

Changeset: bf863df422249b2e614d362459a1ce51357ffc6f

comment:42 Changed 7 years ago by Samuel Jackson

Refs #5421 Added multiple plot option to ResNorm.

Also updated plot to use +/- resolution * 10

Changeset: d9b46df1928a475512aac4409acbff8269d4673d

comment:43 Changed 7 years ago by Samuel Jackson

Refs #5421 JumpFit now plots to the miniplot.

Changeset: 702e7320dbe812c7fa002e11bba7237779fe5275

comment:44 Changed 7 years ago by Samuel Jackson

Refs #5421 Updated JumpFit GUI.

Changeset: 32ff420ef7af1dc24f42a53fd6b307a0038a4716

comment:45 Changed 7 years ago by Samuel Jackson

Refs #5421 Removed default resolution range from Quasi and Stretch.

Changeset: 613a0cf95b6c5fdf8fabed670fb4b457ac8ffdbe

comment:46 Changed 7 years ago by Samuel Jackson

Refs #5421 Updated ResNorm in IndirectBayes.

Changeset: 3fd966f84b0ac75b8ea6fc1b4c88f4ad79216dc3

comment:47 Changed 7 years ago by Samuel Jackson

Refs #5421 Updated interface with better file handling.

Changeset: 77b583c8adc95e517ff0d7db8c287b2d7f68f752

comment:48 Changed 7 years ago by Samuel Jackson

Refs #5421 Updated Bayes GUI ready for JumpFit integration.

Changeset: cc7a0acb9400cdddbbd6a88c05ba426666c5a059

comment:49 Changed 7 years ago by Samuel Jackson

Refs #5421 Updated documentation for interface.

Changeset: 316b206d1def5b4a64a6cc8fb4a3a6675a898a18

comment:50 Changed 7 years ago by Samuel Jackson

Refs #5421 Fixes for system tests.

Changeset: 2688eec584e8a25aeb312c028d3798abbf1f7377

comment:51 Changed 7 years ago by Samuel Jackson

Refs #5421 Updates to Quest and QLRun.

Also swapped using SaveNexus to SaveProcessedNexus.

Changeset: 3f819a7eae01537f6af3941604e32fc797267e19

comment:52 Changed 7 years ago by Samuel Jackson

Merge branch 'feature/5421_IDA_bayes_interface' into develop

Refs #5421

Conflicts:

Code/Mantid/scripts/Inelastic/IndirectBayes.py

Changeset: 308eeb825dc669a097ef5feec606dfa4f4e7a617

comment:53 Changed 7 years ago by Samuel Jackson

Refs #5421 Browsing for files now open the default save directory.

Changeset: f9bd37a467b6bd7dfd3c978e826b6f9443e7aed5

comment:54 Changed 7 years ago by Samuel Jackson

Refs #5421 Missed quotes for string background parameter.

Changeset: 38c12ec7afe17f75095c723bd938757dd455dff5

comment:55 Changed 7 years ago by Samuel Jackson

Refs #5421 Updating system tests.

Changeset: 06094c90762a84248e94af2e025ea04196168a13

comment:56 Changed 7 years ago by Samuel Jackson

Refs #5421 Changed sequential fit to be checked by default.

Changeset: 4ba773e722083d9ecedc2112548546007f793e9b

comment:57 Changed 7 years ago by Samuel Jackson

Refs #5421 Fix ResNorm plotting.

Changeset: 4b56d20a12eae88c8f01233a24ac378111f4b75e

comment:58 Changed 7 years ago by Samuel Jackson

Refs #5421 Remove z-order tags to fix warnings.

Changeset: 61511fd8017a7134d15f86901b1956acc080e564

comment:59 Changed 7 years ago by Samuel Jackson

Refs #5421 Modified JumpFit to plot desired spectrum.

Changeset: 51021dfbcfb785db43de47028e7d352fb7310bb8

comment:60 Changed 7 years ago by Samuel Jackson

Refs #5421 Cosmetic changes to Quasi

Changeset: 2c9e0f6cffa1764ea90a2b82b477fe575dcf8ec6

comment:61 Changed 7 years ago by Samuel Jackson

Refs #5421 Remove redundant bin boundary code.

Changeset: 9003dd31520e92b000e8866c60389cdce9b13ae1

comment:62 Changed 7 years ago by Samuel Jackson

Refs #5421 Fix Quest Plotting and Quasi run function.

Changeset: b497d841687fcd0241253c478ac5a710125fd8f6

comment:63 Changed 7 years ago by Samuel Jackson

Refs #5421 Cosmetic changes to JumpFit

Changeset: da407ef0e382dc7281c87c57191e4199de891688

comment:64 Changed 7 years ago by Samuel Jackson

Merge branch 'feature/5421_IDA_bayes_interface' into develop

Refs #5421

Conflicts:

Code/Mantid/scripts/Inelastic/IndirectBayes.py

Changeset: fae01ce13a986daaa717a3116b239fd34c620bca

comment:65 Changed 7 years ago by Samuel Jackson

Refs #5421 Swapped to using MantidQwtMatrixWorkspaceData

Changeset: 5e46074da93debb2da73bfabca66140a1722d2a4

comment:66 Changed 7 years ago by Samuel Jackson

Refs #5421 Correction to get ResNorm file working.

Changeset: b5a8d357e0b9568450d43249a2457d3f7ead7b5c

comment:67 Changed 7 years ago by Samuel Jackson

Refs #5421 Correcting comments.

Changeset: 970de4cd6a220acad3fcb263322657f7b703f6b2

comment:68 Changed 7 years ago by Samuel Jackson

Refs #5421 Updated interface to respond to change dir notifications.

Changeset: 42062737cf2f94880487b6fb0e642ae74610a3d3

comment:69 Changed 7 years ago by Samuel Jackson

Revert "Refs #5421 Updating system tests."

This reverts commit 06094c90762a84248e94af2e025ea04196168a13.

Changeset: c71f8bdad0ed67d79395071042905541e3adb8d7

comment:70 Changed 7 years ago by Samuel Jackson

Wrong ticket number supplied with commit, see ticket #7965

Last edited 7 years ago by Samuel Jackson (previous) (diff)

comment:71 Changed 7 years ago by Samuel Jackson

Wrong ticket number supplied with commit, see ticket #7965

Last edited 7 years ago by Samuel Jackson (previous) (diff)

comment:72 Changed 7 years ago by Martyn Gigg

Revert "Revert "Refs #5421 Updating system tests.""

This reverts commit c71f8bdad0ed67d79395071042905541e3adb8d7.

It brings back the changes as they should be and allows future merges to develop without further conflicts Refs #5421

Changeset: 53dc57742e82088b4c245ae298e67460141a3ba9

comment:73 Changed 7 years ago by Samuel Jackson

Merge remote-tracking branch 'origin/master' into feature/5421_IDA_bayes_interface

Conflicts:

Code/Mantid/MantidQt/CustomInterfaces/CMakeLists.txt Code/Mantid/scripts/Inelastic/IndirectBayes.py

Refs #5421

Changeset: 814fabbde2a6cdbe4c15acfbdcf66c379a4ed29c

comment:74 Changed 7 years ago by Samuel Jackson

Merge remote-tracking branch 'origin/master' into feature/5421_IDA_bayes_interface

Conflicts:

Code/Mantid/scripts/Inelastic/IndirectBayes.py

Refs #5421

Changeset: 014b3c0e2fe4f9dab420de094b5deab4cd20df74

comment:75 Changed 7 years ago by Samuel Jackson

Refs #5421 More updating bayes for GUI.

Changeset: 29c6613669f89ceb772288b76aaa862b54a9c815

comment:76 Changed 7 years ago by Samuel Jackson

Merge branch 'feature/5421_IDA_bayes_interface' into develop

Conflicts:

Code/Mantid/MantidQt/CustomInterfaces/CMakeLists.txt Code/Mantid/scripts/Inelastic/IndirectBayes.py

Refs #5421

Changeset: a284f0574eb7429cf6b2e75193e6276aeca8318e

comment:77 Changed 7 years ago by Samuel Jackson

Refs #5421 Updated system tests.

Changeset: 909a5d6aa8aef18bd001f094917854c4f7279fd0

comment:78 Changed 7 years ago by Samuel Jackson

Merge branch 'feature/5421_IDA_bayes_interface' of github.com:mantidproject/systemtests into feature/5421_IDA_bayes_interface

Conflicts:

SystemTests/AnalysisTests/ISISIndirectBayesTest.py

Refs #5421

Changeset: f7ed44060c143f58daa6b5d19130c105a54c7932

comment:79 Changed 7 years ago by Samuel Jackson

Refs #5421 Added interface category.

This should fix issues in ticket #7614.

Changeset: c3cc09b081aa7374f45977efce307d806e788a64

comment:80 Changed 7 years ago by Samuel Jackson

Refs #5421 Make ResNorm number non mandatory.

Changeset: 4f8984c51e6f2b24e1ae89342aedc6c26f337fe0

comment:81 Changed 7 years ago by Samuel Jackson

Refs #5421 Tweaks and bugfixes for Bayes interface.

Changeset: 1b68631691eb4b66fe5cc85811c3cf70c9f17971

comment:82 Changed 7 years ago by Samuel Jackson

Refs #5421 Correct bins.

Changeset: 2b7bc6385d243d61767b39d6b1659b688c1c383c

comment:83 Changed 7 years ago by Samuel Jackson

Merge branch 'feature/5421_IDA_bayes_interface' into develop

Conflicts:

Code/Mantid/scripts/Inelastic/IndirectBayes.py

Refs #5421

Changeset: 27619991623ea687d853cbbb30818d1037799c30

comment:84 Changed 7 years ago by Samuel Jackson

-snip- Wrong ticket number

Last edited 7 years ago by Samuel Jackson (previous) (diff)

comment:85 Changed 7 years ago by Samuel Jackson

Refs #5421 Add labels to output plots.

Changeset: 0f5e9b505c1b50832f9bab18ac45a63ed05c335c

comment:86 Changed 7 years ago by Samuel Jackson

To Tester

This interface pulls together the indirect bayes workflow algorithms. You need to check that each of the tabs in the interface works as it should. For inspiration for valid input data I would look at the system tests in ISISIndirectBayesTest.py. I should note that Quasi runs the QLines routine and Stretch runs the Quest routine. If you need any further clarification of how to use the interface just ask.

ResNorm This uses an indirect *_red file and a *_res file. There is a pair of these in the system tests repo. (irs26176_graphite_002_red and irs26173_graphite_002_res).

Quasi As above, but the resolution option can either be a *_res file or a *_red (e.g. irs26173_graphite_red). It can also optionally take a width file (e.g. irs26176_graphite002_width_water.dat) and a res norm file (generated on the res norm tab).

Stretch As ResNorm.

JumpFit JumpFit takes the output of *_Workspace from either Quasi (when run with lorentzians option) or a sequential ConvFit with one or two lorentzians.

Remember to merge both the System tests and the main repo in to master

Last edited 7 years ago by Samuel Jackson (previous) (diff)

comment:87 Changed 7 years ago by Samuel Jackson

  • Status changed from inprogress to verify
  • Resolution set to fixed

comment:88 Changed 7 years ago by Peter Parker

  • Status changed from verify to verifying
  • Tester set to Peter Parker

comment:89 Changed 7 years ago by Samuel Jackson

Refs #5421 Fix output workspace names.

Changeset: 6d121781c9b205ae638ea5bd525251691c828a41

comment:90 Changed 7 years ago by Samuel Jackson

  • Status changed from verifying to reopened
  • Resolution fixed deleted

comment:91 Changed 7 years ago by Samuel Jackson

  • Status changed from reopened to verify
  • Resolution set to fixed

comment:92 Changed 7 years ago by Samuel Jackson

  • Status changed from verify to reopened
  • Resolution fixed deleted

comment:93 Changed 7 years ago by Samuel Jackson

  • Status changed from reopened to inprogress

Refs #5421 Remove extra underscore for system tests.

Changeset: 6bb77d40147bfbbdb58e613777a60c18e156427e

comment:94 Changed 7 years ago by Samuel Jackson

  • Status changed from inprogress to verify
  • Resolution set to fixed

comment:95 Changed 7 years ago by Peter Parker

  • Status changed from verify to verifying

comment:96 Changed 7 years ago by Samuel Jackson

  • Status changed from verifying to closed

Merge branch 'feature/5421_IDA_bayes_interface' of github.com:mantidproject/mantid into feature/5421_IDA_bayes_interface

Full changeset: ​14c4d6538a967c9414cf3955db15f24b142676cc

comment:97 Changed 7 years ago by Samuel Jackson

Merge branch 'feature/5421_IDA_bayes_interface' of github.com:mantidproject/mantid into feature/5421_IDA_bayes_interface

Full changeset: ​bcdddf61ae56efa0b6df92c375ca092920003fa9

comment:98 Changed 7 years ago by Peter Parker

Merge remote-tracking branch 'origin/feature/5421_IDA_bayes_interface'

Full changeset: ​c43a8c5af7d627e87395e69ea082c0d33e47a41d

comment:99 Changed 7 years ago by Samuel Jackson

Merge branch 'feature/5421_IDA_bayes_interface' of github.com:mantidproject/systemtests into feature/5421_IDA_bayes_interface

Conflicts:

SystemTests/AnalysisTests/ISISIndirectBayesTest.py

Refs #5421

Full changeset: ​f7ed44060c143f58daa6b5d19130c105a54c7932

comment:100 Changed 7 years ago by Peter Parker

Merge remote-tracking branch 'origin/feature/5421_IDA_bayes_interface'

Full changeset: ​176370ad0b24709ab22aa49613c7e82f1889986a

comment:101 Changed 7 years ago by Peter Parker

The new interface seems to work as expected. I can't comment on the correctness of the results, but the system tests are now passing. The code looks good.

In a couple of places I ran into issues to do with the default save directory not having a trailing separator. I have opened #8243 to deal with this issue.

comment:102 Changed 5 years ago by Stuart Campbell

This ticket has been transferred to github issue ​6267

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