- edited description
Mapping request, study and acquisition names to standard names
Add the ability to map each request, study and acquisition name to a user-defined name.
This will enable easy dose comparison between systems where the same clinical exposures use different names.
Charts of user-defined names vs. dose metrics will have to be produced.
Required to enable work on #598
I would like charts of standard acquisition name and also of standard study name. I would like standard study / request / procedure name pooled together into one. So if a particular study description and requested procedure name share the same standard name, I would like the data from both to be included in a chart which shows that standard name
So far:
- An admin user can enable or disable the standard name mapping feature
- An admin user can define standard names for each modality, each associated with a study description, procedure name, requested procedure name or acquisition protocol
- Multiple study descriptions, procedure names, requested procedure names or acquisition protocols can be mapped to a standard name all at once
- If the standard name mapping feature is enabled then users can filter the data in the summary views by standard study, procedure, request and acquisition names
- CT, radiography, mammography and fluoroscopy charts of standard acquisition / study name
- When clicking on “Modify” for a standard name entry, make the modification page pick up all study descriptions, procedure names, requested procedure names and acquisition protocols associated with that name
- Import routines associate any relevant standard name with the study on import for all modalities
- Standard name data now included in exports (not tested)
- xlsx exports now include a worksheet for each standard acquisition protocol, prefixed with “[standard]“
To do:
- Add some tests
- Write some documentation
Comments (154)
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reporter Added skeleton form to enable a user to enter a standard name. Need to populate the other fields with drop-down options based on existing database contents. May need a form for each modality. Also need a view to show the user all the existing standard names (probably a bit like the display name page). Refs issue
#862→ <<cset f579a6122f9c>>
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reporter Trying to make adding standard name CT-specific. Not finished yet. Refs issue
#862→ <<cset 62eb07984a62>>
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reporter Adding lists of existing values to the form fields. Refs issue
#862→ <<cset ad8e8a09bc09>>
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reporter Form now adds a row to the standard name database table. Refs issue
#862→ <<cset a7d29d9625a6>>
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reporter If form is unchanged then don't add an entry to the standard names table. Refs issue
#862→ <<cset 45303a7452df>>
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reporter Adding modality as a hidden field so that I can use the modality to customise the URL, like /add_new/ct; /add_new/dx etc (not implemented yet). Refs issue
#862→ <<cset 5e84ba982f72>>
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reporter Added radiographic standard name form. Need to make the acquisition protocol names DX/CR-specific. Refs issue
#862→ <<cset 32d5dd79d779>>
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reporter Acquisition protocols on radiographic standard name form now DX/CR/PX-specific. Refs issue
#862→ <<cset 4dc59d31d12b>>
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reporter Made the title of the form more user-friendly. Removed the MODALITIES CommonVariable that I don't think I need. Refs issue
#862→ <<cset d8e2e21ee007>>
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reporter Added mammography and fluoroscopy standard name forms. Refs issue
#862→ <<cset 64d2a7c3ad17>>
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reporter Moved field value initialisation inside the CT form to see if this helps with the build error. Refs issue
#862→ <<cset 4f67a547ba78>>
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reporter Moved field values inside initialisation seems to have worked for CT, so doing the same for the other modalities. Refs issue
#862→ <<cset defcc4abb997>>
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reporter Added views to show the current standard names. Based on the display name code - needs updating, but does show the standard names. Need to make it possible to edit or delete a current entry. Refs issue
#862→ <<cset 112295ef5a0e>>
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reporter Added buttons for modifying or deleting an entry (they don't do anything yet). Refs issue
#862→ <<cset c9b3b5773be4>>
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reporter Added ability to delete an entry from the standard names. Refs issue
#862→ <<cset a216376800b5>>
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reporter Added ability to modify a standard name entry. Added links from standard name table to the delete and modify pages. Added a link in the Config menu to the standard name page. Refs issue
#862→ <<cset f1a75ad6dd83>>
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reporter I'm wondering about using the RSNA RadLex as a built in set of standard names (https://www.rsna.org/practice-tools/data-tools-and-standards/radlex-radiology-lexicon). Thoughts @Ed McDonagh ?
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reporter Added a system-level setting to configure if standard names should be used. Added display of standard names in the CT summary page. Modified standard name table so that a requested procedure name, study description, procedure name and acquisition protocol can only appear in the table once - not sure if this will cause issues. It may be that these fields should be unique with modality, rather than just unique on their own. Refs issue
#862→ <<cset 7c39ab6e3850>>
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reporter Adding form template that I forgot to commit. Refs issue
#862→ <<cset 28dca649b50c>>
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reporter Importing the exception that I think is causing the tests to fail. Refs issue
#862→ <<cset 2802a23254e1>>
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reporter Added display of standard acquisition protocol in the detailed CT view. Created check for empty fields in the standard name forms to ensure that None is returned, otherwise an empty string is stored in the database and causes issues with the unique field constraints. Refs issue
#862→ <<cset efb0864afe36>>
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reporter Added a standard name base form, and using this as the basis for the modality-specific ones. Any existing entries in the standard name table are removed from the form options. For example, if the requested procedure name CT head already appears in a standard name, then CT head will not appear in the drop down list of requested proecdure names when creating a new CT standard name. Refs issue
#862→ <<cset 9cffaec69294>>
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reporter Added standard name display to the DX summary and detailed views. Refs issue
#862→ <<cset cf1e6ce76032>>
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reporter Added standard name display to the mammography and fluoroscopy summary and detailed views. Refs issue
#862→ <<cset c442741b7253>>
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Looking good @David Platten
It would be good to have something other than
None
appear in the menus and tables - not sure if it isAny
maybe? Though that wouldn’t apply in the filter list pages.Regarding RadLex, how would this be surfaced? My concern about RadLex, and I’m not sure it is a valid concern or not, is whether for a UK audience it is too American, and for a non-English audience whether it is useful at all. But either way, I presume you could just ignore it? Would there be a facility to load up an alternative localised version, either in a future release or at an institution level?
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reporter Enforcing modality on standard name lookups in the filtered and detailed views. Refs issue
#862→ <<cset 30dbd62d7c95>>
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reporter Allowing current value to appear in the options if the user is modifying an existing entry. Refs issue
#862→ <<cset 64085891bcbe>>
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reporter Consistently labelling the form / column headings. Fixed error introduced in a previous commit that broke the build. Refs issue
#862→ <<cset 9c2b55a46e08>>
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reporter Correcting some instances of enable_standard_names variable. Refs issue
#862→ <<cset 1414470f0a2f>>
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reporter Added filters for standard study, procedure and requested procedure to each modality summary view. Refs issue
#862→ <<cset 3d287c32183c>>
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reporter Added filters for standard acquisition protocol to each modality summary view. Refs issue
#862→ <<cset a67f98a4df63>>
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reporter Making study description, procedure name, requested procedure name and acqisition protocol unique per modality in the standard name table. They were globally unique, so if a DX study description matched a CT study description then you could only use it for one of the two modalities. Refs issue
#862→ <<cset b3d8b3a646ee>>
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reporter - edited description
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reporter - edited description
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reporter - edited description
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reporter Added skelton CT bar chart of standard study name - no data provided for this yet. Replaced the standard study, procedure and requested procedure name filters with one standard study filter. Refs issue
#862→ <<cset 13694c0443c1>>
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reporter Added CT bar chart of standard study name - mean and median implemented. There's something wrong with the standard name filtering at the moment. Refs issue
#862→ <<cset 62f7244c634c>>
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reporter The filtering does work - it just provided a strange result due to the way I have configured my standard names at the moment.
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reporter Fixed the failing tests - switched off the new chart by default. Refs issue
#862→ <<cset e2f4f273efb5>>
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reporter Refactored out a method to create a DataFrame of standard_study data - will be useful for other chart routines such as boxplot and histogram. Refs issue
#862→ <<cset 66a407ba90bd>>
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reporter Reverted create_dataframe_aggregates to original code. Using create_standard_study_df in the view_charts code and passing this data frame to the chart function. Boxplot and histogram CT standard name charts now working. Refs issue
#862→ <<cset 726f200a017a>>
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reporter Added CT standard study frequency chart. Moved creation of standard study dataframe so that it is only calculated once, rather than for each chart. Refs issue
#862→ <<cset f0bee192586e>>
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reporter Added CT standard study workload chart. Rearranged order of CT charts so they appear on the screen in the same order as they appear in the chart options. Refs issue
#862→ <<cset 90b485abe4ae>>
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reporter Added CT standard study DLP over time chart. Refs issue
#862→ <<cset 6b95b8dd0b44>>
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reporter Reordered the CT standard name charts so that the workload chart is at the bottom, the same as for the study description chart order. Refs issue
#862→ <<cset f947dfe39e19>>
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reporter Added standard study CT events chart. Corrected typo in study description events histogram filename. Refs issue
#862→ <<cset 2576b5d45ae6>>
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reporter Only include standard study charts in the required list if the standard names feature is enabled. Added a horizontal bar at the start of the standard name chart options on the CT filtered page and the general chart options page. Refs issue
#862→ <<cset 6a560a723583>>
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reporter Fixing failed tests. Need to enable standard mapping in the CT tests now. Fixed typo in one of chart methods. Refs issue
#862→ <<cset 30627d45d54a>>
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reporter Fixing failed tests - again. Importing the required exception. Refs issue
#862→ <<cset 743f0e1c10f2>>
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reporter Corrected tag error in CT filtered page. Refs issue
#862→ <<cset e0db5652bff5>>
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reporter Collapsed the CT chart options on the CT filtered page into categories. This tidies up the options part of the page, I think. Refs issue
#862→ <<cset 85dccc600bc8>>
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reporter Setting the class of the CT options tables so that they occupy the full width of the div. Refs issue
#862→ <<cset 6bae5e8c82d9>>
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reporter Moved the over-arching plot charts option out of a collapsable list so it is always visible. Refs issue
#862→ <<cset dc260f6fca64>>
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reporter Added CT chart of standard acquisition name DLP. Refs issue
#862→ <<cset 9b5fd51538ef>>
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reporter Removing blank entries from the standard acquisition name DLP charts. Refs issue
#862→ <<cset fa7d1818a82d>>
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reporter Added CT chart of standard acquisition name frequency. Solved issue of blank still appearing - needed to remove the unused category. Refs issue
#862→ <<cset 381ee5d5ee95>>
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reporter Refactored creation of mean, median, boxplot and histogram chart into a method for the CT charts. Sort of refs issue
#862→ <<cset 4dd9c1bfe841>>
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reporter Removed unnecessary standard study custom filter. Made modality lookup for standard names exact rather than iexact. Refs issue
#862→ <<cset aa9517d890d9>>
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reporter Correcting typo from an earlier commit where I used 'field=' instead of 'field_name=' - this caused the DX, RF and MG filtered pages to break. Refs issue
#862→ <<cset 57eaf82f24dd>>
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reporter Grouped mammo chart options. Replaced acquisition AGD chart code with the refactored method. Refs issue
#862→ <<cset b7eb586a92df>>
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reporter Grouped radiographic chart options. Fixed bug in generate_average_chart_group - it had a CT-specific user profile option. Refs issue
#862→ <<cset f314a2d3b8d9>>
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reporter Replaced radiographic chart code with the refactored method. Refs issue
#862→ <<cset 850960d7303b>>
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reporter Added CT chart of standard acquisition name CTDI. Refs issue
#862→ <<cset 373792a947ef>>
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reporter Added CT charts of standard acquisition name CTDI and DLP over time. Refs issue
#862→ <<cset 7bbb8eee362a>>
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reporter Added CT charts of standard acquisition name CTDI and DLP vs mass. Refs issue
#862→ <<cset d0416e8368b4>>
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reporter - edited description
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reporter Using a many to many relationship for the standard names. Massive speed increase. Not finished yet, but CT should work (not sure if the tests will pass). Sort of refs issue
#862→ <<cset ad36b350800f>>
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reporter Removing blank standard names from the dataframe for the standard name charts. Refs issue
#862→ <<cset ac029f9b9c79>>
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reporter Changed how standard names are added, updated and deleted to increase speed. Refs issue
#862→ <<cset 004d2a30ecfc>>
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reporter Updated acqusition protocol standard names to match method of study-level ones. Need to update CT standard protocol charts to use the new data. Refs issue
#862→ <<cset 026f47502b26>>
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reporter Updated the CT acquisition filters and charts to use the many to many field. Removed redundant checks for presence of acquisition level filters which related to the old HighCharts plots in CT and DX. Refs issue
#862→ <<cset 8d0417a4b5fa>>
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reporter - edited description
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reporter Correcting bug where the std_field_name variable does not exist. Refs issue
#862→ <<cset e64c679929cb>>
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reporter Added JavaScript to add, update and delete form submit buttons so that the user is warned that database is being updated and it may take a while. Refs issue
#862→ <<cset f45cc85c4307>>
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reporter Updated acquisition-level standard name updating and adding to ensure that only the required modality items in IrradEventXRayData.objects are changed. Updated MG and RF pages to use the manytomany standard names. Refs issue
#862→ <<cset 8aae76076379>>
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Is it possible to select multiple names for mapping simultaneously? When I last installed this branch, trying to select each of the CT TAP protocols one at a time was a bit frustrating! Worth doing, but could be nicer.
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reporter Corrected bug where if a user cancelled the form it caused an error. Disabled cancel button on form once a user has clicked submit. Refs issue
#862→ <<cset 5303d373b3dc>>
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reporter Can now add standard names to multiple study descriptions, requested procedures, procedures and acquisition protocols. Refs issue
#862→ <<cset f0ff1c5f4b4a>>
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reporter - edited description
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reporter Changed the form for adding and modifying standard names. Uses a layout similar to the Django user admin pages. Making use this multiselect JavaScript library: http://loudev.com/ and this JavaScript quicksearch library: https://github.com/riklomas/quicksearch. Need to modify the display of standard names so that there is one row per standard name showing all study descriptions etc that are associated with it. Also need to modify the updating page so that it shows all the currently selected items for that standard name. Refs issue
#862→ <<cset 8d926865702c>>
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Is it safe to use that quicksearch library - the author has marked it as very much dead. Is there a maintained fork? Is that what Django are using?
(BTW, the full stop has messed up the link to https://github.com/riklomas/quicksearch )
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reporter Hi @Ed McDonagh you are right that the quicksearch is defunct. I’ve just found this, which I’ll look to use instead: https://www.npmjs.com/package/jquery.quicksearch
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reporter @Ed McDonagh I didn’t answer your other question. Django isn’t using the method I have implemented on the user pages. That method is specific to the admin view, and I cannot get it to work on a non-admin page. I’ve done a fair bit of searching and haven’t found an example that uses the admin view’s method on a non-admin form that works for me.
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Might be the best to go with, but it’s still had no love for about four years.
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reporter Updated standard study name addition and modify pages to use exactly the same code as that used by the Django user admin page. Refs issue
#862→ <<cset 6742b4fc1d09>>
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reporter Enabled a standard user to view the standard name mappings, but not add new entries or modify existing ones. Refs issue
#862→ <<cset 799e4a7e0a76>>
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reporter Standard name view now groups entries so each standard name appears one. The Modify and Delete buttons now work as expected. It's possible to increase the efficiency of the Modify button code so that only changed data is updated / added - at the moment a blanket approach is used. Refs issue
#862→ <<cset cc1f23d44f8e>>
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reporter Sorted study descriptions etc into alphabetical order in each cell of a standard name row. Refs issue
#862→ <<cset cbe10a0c6517>>
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reporter - edited description
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reporter Made the standard name pages work for DX, MG and RF modalities. Refs issue
#862→ <<cset 066041d5a93a>>
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reporter Removed unrequired graphic file. Refs issue
#862→ <<cset b3518c3f4865>>
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reporter Improved the logic of the standard name code to add and modify entries. Refs issue
#862→ <<cset f2c56b2ad5c2>>
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reporter Grouped fluoroscopy chart options on the filtered view. Made all filtered view chart options visible by default (they can then be collapsed by the user by clicking on the heading). Refs issue
#862→ <<cset 67d3cfce6a65>>
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reporter Added standard protocol name charts for radiography. Refs issue
#862→ <<cset 597b011a46c2>>
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reporter Added standard study name charts for radiography. Also changed check for empty queryset from 'if not f.qs' to 'if not f.qs.exists()' - this is much quicker to execute. Refs issue
#862→ <<cset 9975b6c68aea>>
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reporter Added index to unique_equipment_name to speed up chart queries. Refs issue
#862→ <<cset a90b82b43fe0>>
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reporter Some optimisation on chart queries when just standard name charts are selected: any None standard name entries are excluded from the queryset before creation of the dataframe. This increases speed. Refs issue
#862→ <<cset 836098536101>>
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reporter Check for required standard name charts before trying to exclude data from the standard name dataframe. Fixes the failed test (on my local machine at least). Refs issue
#862→ <<cset 219c0aac8270>>
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reporter Added mammo standard acquisition level charts. Still need to add the study one. Refs issue
#862→ <<cset 93263620cde0>>
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reporter Added mammo standard study level chart. Refs issue
#862→ <<cset 1606ac126d0f>>
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reporter Added fluoroscopy standard name charts. Refs issue
#862→ <<cset a8a53feae118>>
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reporter Made overflow auto for the value selection boxes on the add / modify standard name mapping page. Some of my fluoro names are long so it's good to be able to scroll to read them. Refs issue
#862→ <<cset 4abd5e072b56>>
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reporter Added check for standard names when choosing the fluoroscopy chart summary list filter. Refs issue
#862→ <<cset 62bdd08aad97>>
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reporter - edited description
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reporter Added code to add standard name references on study import. Refs issue
#862→ <<cset 6efadca55ba1>>
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reporter Moved location of add_standard_names in the dx and mam extractors to ensure it is run for each study. Refs issue
#862→ <<cset 7bba425c0ebf>>
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reporter Addressing some Codacy issues. Refs issue
#862→ <<cset b393a97b5880>>
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reporter Addressing some more Codacy issues. Refs issue
#862→ <<cset c96f27c5a2a6>>
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reporter Fixing mod_filters problem that I caused with my over-zealous changes in the previous commit. Refs issue
#862→ <<cset 128b71880ec0>>
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reporter Attempting to add study- and request-related standard names to the exports. Refs issue
#862→ <<cset 468ef323239b>>
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reporter Adding standard acquisition names to exports. Tested CT, but not the other modalities. Need to add an option to enable a worksheet per standard acquisition name, rather than per protocol. Refs issue
#862→ <<cset 9115b75df8de>>
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reporter Fixing bugs - didn't create the enable_standard_names variable. Refs issue
#862→ <<cset 0641e0bd1caa>>
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reporter - edited description
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reporter Fixed RF exports when standard names activated. Refs issue
#862→ <<cset bd6dcc2f09c8>>
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reporter Trying to fix RF exports when standard names activated. Frequency of study descriptions and requested procedures remains incorrect on the summary page of the xlsx file. Refs issue
#862→ <<cset 163a40500df6>>
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reporter Solved the issue of study descriptions, requested procedure names and standard names being counted multiple times in the export summary sheet whenever a values was entered in the standard acquisition name filter. This was affecting all modality exports. Refs issue
#862→ <<cset 0576ff14aac0>>
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reporter Adding this line to my local_settings.py has been really useful when debugging the export routines:
CELERY_TASK_ALWAYS_EAGER = True
It forces the delayed celery tasks to run in the same thread as the main python, making it easy to insert breakpoints and debug any code that is usually a delayed action.
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That’s really a useful tip. One of those things we need to add to the developer docs!
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reporter Removing code that excluded studies with null standard acquisition names from the chart queryset if just standard acquisition protocol charts were being asked for. This didn't work as I expected because the exclusion removes studies if any acqusition in that study has a null standard acquistion name, rather than exlcuding the study only if all of the acquisitions have a null standard acquisition name. Thanks to my colleage Rory for testing the system and pointing out this problem. Refs issue
#862→ <<cset 0f460618b279>>
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reporter Moved aggregated dataframe creation within the mean and median if statement - only need to create it for these. Will speed up code when just boxplots or histograms are required. Refs issue
#862→ <<cset ebd7e1a30623>>
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reporter Added a datatable below each CT bar chart. Sort-of refs issue
#862→ <<cset 6eb17955a7f7>>
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reporter Simplified the JavaScript a little and added some comments. Sort-of refs issue
#862→ <<cset 6fab1fb9a305>>
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reporter Improving table titles, replacing NaN with - in the table, switching off escape of special characters so that CTDIvol is correctly subscripted in the table headings. Sort-of refs issue
#862→ <<cset 00c9f1528349>>
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reporter Improving data tables: pivoted so now a column per x-ray system for value and count. Formatting improved. Sort-of refs issue
#862→ <<cset ac3bd87e3239>>
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reporter @Ed McDonagh I’m unsure of how to update the export feature. I have already included standard study names and standard acquisition names in the existing export documents.
The existing xlsx export routines create a worksheet for each acquisition protocol name. I would like the user to be able to select an export where a worksheet is created for each standard acquisition name, but am unsure about how to do this. Do you have any guidance?
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I guess there’s three options?
- Where you configure standard names on/off, also determine whether standard names are used instead of original names where available in exports
- Duplicate set of export buttons to export with standard names instead of original
- Export both somehow!
I think what is probably want is tabs with standard names where they exist, but a standard name and an original name column in the sheets.
Does this help in any way? Or am I barking up the wrong tree?
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reporter Thanks @Ed McDonagh that’s helpful.
I think I’ll go with creating worksheets for both if the standard names option is switched on. I’ll have to prefix the standard name sheets with something in case a standard name is exactly the same as a regular acquisition name. Perhaps “Std name: “.
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reporter Added standard acquisition name data to the summary page of the xlsx file. Refs issue
#862→ <<cset 421c73d2f903>>
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reporter Added export of standard acquisition name data to their own tabs in xlsx workbooks. Refs issue
#862→ <<cset c3d8090d2aa7>>
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reporter - edited description
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reporter Removing the max_length of the procedure_code_meaning field. The restriction is causing problems with my test system where I have updated this field with longer-than-usual names. Refs issue
#862→ <<cset 5a5ae7ef9a58>>
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reporter @Ed McDonagh we have been using this branch on a test server to come up with local DRLs using the standard name mapping feature. We think it works well. The feature needs documentation writing, and perhaps some tests, otherwise it is good to go.
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reporter -
assigned issue to
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assigned issue to
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Hmm. I just tried migrating my database to the new develop merged branch and it is not working.
makemigrations
seemed happy, butmigrate
is complaining:Running migrations: Applying remapp.0016_auto_20220519_0903...Traceback (most recent call last): File "/home/mcdonaghe/research/vep38/lib/python3.8/site-packages/django/db/backends/utils.py", line 82, in _execute return self.cursor.execute(sql) psycopg2.errors.DuplicateTable: relation "remapp_standardnames" already exists
I don’t know yet if that means the table is already in the database (in which case why didn’t
makemigrations
say so) or if there is an issue with the inter-table relationships… -
I do have a StandardNames table in my database (via PGAdmin), and it has one row in. I wonder why makemigrations thinks it needs to be added again? I’ll delete all my migration files and try again.
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Hmm… different issue now, it is trying to remake the Jannis tables! Same error!
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Re-refactoring stuff Jannis had refactored. Moving Tasks to bottom of config list again. Refs
#862→ <<cset 7339856a80cc>>
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Further refactoring. RF and MG filter list are different, not sure why... Refs
#862→ <<cset e5409a10f78e>>
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Black. Refs
#862→ <<cset 5e8b9740ce11>>
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Codacy. Refs
#862→ <<cset 9e5812393862>>
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More nosec for mark_safe() for Codacy. Black had moved them to the wrong lines. Refs
#862→ <<cset 44375dabad90>>
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Merged in issue862moreRefactoring (pull request #506)
Refs
#862. Adds more refactoring into pull request #505→ <<cset b73179a463cd>>
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Minor codacy changes. Refs
#862→ <<cset 8e7342daf0c0>>
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reporter Removing redundant method from chart_functions.py. Refs issue
#862→ <<cset ba2457b198ee>>
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reporter Disabling line-too-long pylint for some chart code. Refs issue
#862→ <<cset 814a027c56c6>>
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reporter Trying to disable line-too-long pylint for some chart code. Refs issue
#862→ <<cset 2c354b63a9c2>>
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- changed status to resolved
Merged in developIntoIssue862StandardNameMapping (pull request #505)
Fixes
#862NM standard name mapping to be covered in issue ref #938
→ <<cset 24a9a2e55d0f>>
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Added ref
#862to changes. [skip ci] docs only→ <<cset 2ea0bb615145>>
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@David Platten can you take a look at dev.openrem.org and tell me if there is a reason I get nothing in the “Chart of standard study name mean DLP” (CT, filtering and chart options are in the link)
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Sorry, scrap that. Shift-Ctrl-r sorted it.
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I don’t think we have an issue for documentation for this do we @David Platten ?
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reporter No, I don’t think so. I have a colleague who is going to look at this for us.
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Brilliant
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