{"action":"created","issue":{"url":"https://api.github.com/repos/4Quant/COPD-staging/issues/72","repository_url":"https://api.github.com/repos/4Quant/COPD-staging","labels_url":"https://api.github.com/repos/4Quant/COPD-staging/issues/72/labels{/name}","comments_url":"https://api.github.com/repos/4Quant/COPD-staging/issues/72/comments","events_url":"https://api.github.com/repos/4Quant/COPD-staging/issues/72/events","html_url":"https://github.com/4Quant/COPD-staging/issues/72","id":151161562,"number":72,"title":"blocking on ","user":{"login":"drtjre","id":16701211,"avatar_url":"https://avatars.githubusercontent.com/u/16701211?v=3","gravatar_id":"","url":"https://api.github.com/users/drtjre","html_url":"https://github.com/drtjre","followers_url":"https://api.github.com/users/drtjre/followers","following_url":"https://api.github.com/users/drtjre/following{/other_user}","gists_url":"https://api.github.com/users/drtjre/gists{/gist_id}","starred_url":"https://api.github.com/users/drtjre/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/drtjre/subscriptions","organizations_url":"https://api.github.com/users/drtjre/orgs","repos_url":"https://api.github.com/users/drtjre/repos","events_url":"https://api.github.com/users/drtjre/events{/privacy}","received_events_url":"https://api.github.com/users/drtjre/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/4Quant/COPD-staging/labels/bug","name":"bug","color":"fc2929"}],"state":"open","locked":false,"assignee":null,"milestone":{"url":"https://api.github.com/repos/4Quant/COPD-staging/milestones/16","html_url":"https://github.com/4Quant/COPD-staging/milestones/COPD-Staging%20Final%20Tests%20-%20Prepare","labels_url":"https://api.github.com/repos/4Quant/COPD-staging/milestones/16/labels","id":1731096,"number":16,"title":"COPD-Staging Final Tests - Prepare","description":"To conclude the COPD-Staging Project, the following set of tests must be passed:\r\n\r\nInitial condition: OSIRIX PACS running on YETI populated with dataset of 200+ COPD CT Thorax exams (Stolz45 and Stolz174 combined datasets)\r\nTest 1:\r\nFrom a spreadsheet of 43 Patient Names (\"Stolz45\"), find a list of studies/sequences of interest using the 4Quant package (Raqea+pacstool)\r\nRequest quantitative data, Lung Volume, PD15, LAA-950, for all 43 studies.  \r\nComparing results, confirm that these values approach values previously calculated for this set in the semi-automatic manor (values compiled for Stolz for publication in early Jan2016).\r\nTest 2:\r\nFrom a spreadsheet of 200 Patient names (Stolz200+), find a list of studies/sequences of interest using the 4Quant package (Raqea+pacstool).\r\nRequest quantitative data, Lung Volume, PD15, LAA-950, for all 200 studies.  \r\nSelect 10 studies at random form these as a sub-sample.\r\nRequest intermediate image data showing Lung Segmentation for 10 sub-samples and Check for appropriateness.\r\nCompare results for these 10 to previously calculated data from the Stolz200+ study.\r\n","creator":{"login":"drtjre","id":16701211,"avatar_url":"https://avatars.githubusercontent.com/u/16701211?v=3","gravatar_id":"","url":"https://api.github.com/users/drtjre","html_url":"https://github.com/drtjre","followers_url":"https://api.github.com/users/drtjre/followers","following_url":"https://api.github.com/users/drtjre/following{/other_user}","gists_url":"https://api.github.com/users/drtjre/gists{/gist_id}","starred_url":"https://api.github.com/users/drtjre/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/drtjre/subscriptions","organizations_url":"https://api.github.com/users/drtjre/orgs","repos_url":"https://api.github.com/users/drtjre/repos","events_url":"https://api.github.com/users/drtjre/events{/privacy}","received_events_url":"https://api.github.com/users/drtjre/received_events","type":"User","site_admin":false},"open_issues":4,"closed_issues":3,"state":"open","created_at":"2016-04-26T05:35:55Z","updated_at":"2016-04-26T15:12:20Z","due_on":"2016-04-29T22:00:00Z","closed_at":null},"comments":0,"created_at":"2016-04-26T15:12:20Z","updated_at":"2016-04-27T09:52:20Z","closed_at":null,"body":"Sending PACS fetched images to \"Segment Lung Tissue\" plugin causes a popup \"This  \r\n\r\n\r\n### Working for File images\r\nLoading images from local filesystem appears to work fine:\r\n```\r\nselect name,mean(run2(image,\"Segment Lung Tissue\",\"\")) from demotable;\r\n+--------------------------------------+---------------------+--+\r\n|                 name                 |         _c1         |\r\n+--------------------------------------+---------------------+--+\r\n| 00SquareLung10by10.tif               | 2709.1330645161293  |\r\n| 01SquareLung10k.tif                  | 1882.0313530871406  |\r\n| 02TwoSquare9522.tif                  | 1836.6011049723757  |\r\n+--------------------------------------+---------------------+--+\r\n3 rows selected (1.482 seconds)\r\n```\r\n\r\n### Loading Images from PACS produces \"Plugin requires a Stack\" Error\r\n\r\n1. Load Images from CSVfedPACS to Table and confirm data loaded successfully\r\n```\r\nCREATE TEMPORARY TABLE Stolz3 USING fourquant.pacs\r\nOPTIONS (bind \"YETI\", username \"OSIRIX\", server \"localhost\", port \"11112\", path \"Stolz3.csv\");\r\n\r\nselect PatientID,SeriesDescription,success from Stolz3 where success=true;\r\n+----------------+--------------------------+----------+--+\r\n|   PatientID    |    SeriesDescription     | success  |\r\n+----------------+--------------------------+----------+--+\r\n| USB0003152149  | Thorax 1.0 I26f 3        | true     |\r\n| USB0002342759  | Thorax nativ 1.0 I26f 3  | true     |\r\n| USB0002387773  | Thorax 3.0 I31f 3        | true     |\r\n| USB0003138461  | Monitoring 10.0 B31f     | true     |\r\n+----------------+--------------------------+----------+--+\r\n4 rows selected (0.21 seconds)\r\n\r\n\r\n```\r\n2. Test CSVfedPACS  Table with simple image fetching and simple calculation\r\n```\r\nselect patientID,seriesDescription,\r\nmean(run2(fetch_dicom_imagej(studyInstanceUID,seriesInstanceUID),\"Median...\",\"radius=3\")) \r\nfrom Stolz3  WHERE success=true;\r\n+----------------+--------------------------+----------------------+--+\r\n|   patientID    |    seriesDescription     |         _c2          |\r\n+----------------+--------------------------+----------------------+--+\r\n| USB000xxx49  | Thorax 1.0 I26f 3        | -514.5741386413574   |\r\n| USB00xxxd59  | Thorax nativ 1.0 I26f 3  | -581.5818977355957   |\r\n| USB000xxx73  | Thorax 3.0 I31f 3        | -551.8430023193359   |\r\n| USB00xxx461  | Monitoring 10.0 B31f     | -400.28540420532227  |\r\n+----------------+--------------------------+----------------------+--+\r\n4 rows selected (3.858 seconds)\r\n\r\n```\r\n\r\n3. Now Substitute Measure with Segment Lung Tissue\r\n```\r\nselect patientID,seriesDescription,\r\nmean(run2(fetch_dicom_imagej(studyInstanceUID,seriesInstanceUID),\"Segment Lung Tissue\",\"\")) \r\nfrom Stolz3  WHERE success=true;```\r\n\r\n-> Popup \"This Command requires a Stack\"\r\n```\r\nWhile, I could modify the plugin to not require a stack, the data should actually be a stack.  \r\nrecommendations?\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/4Quant/COPD-staging/issues/comments/215033842","html_url":"https://github.com/4Quant/COPD-staging/issues/72#issuecomment-215033842","issue_url":"https://api.github.com/repos/4Quant/COPD-staging/issues/72","id":215033842,"user":{"login":"kmader","id":116120,"avatar_url":"https://avatars.githubusercontent.com/u/116120?v=3","gravatar_id":"","url":"https://api.github.com/users/kmader","html_url":"https://github.com/kmader","followers_url":"https://api.github.com/users/kmader/followers","following_url":"https://api.github.com/users/kmader/following{/other_user}","gists_url":"https://api.github.com/users/kmader/gists{/gist_id}","starred_url":"https://api.github.com/users/kmader/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kmader/subscriptions","organizations_url":"https://api.github.com/users/kmader/orgs","repos_url":"https://api.github.com/users/kmader/repos","events_url":"https://api.github.com/users/kmader/events{/privacy}","received_events_url":"https://api.github.com/users/kmader/received_events","type":"User","site_admin":false},"created_at":"2016-04-27T09:52:20Z","updated_at":"2016-04-27T09:52:20Z","body":"I will take a look, it must be related to how the stacks you have are formatted, I'll try to make a better test for it"}}