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main:bgqprocessasampleset [2018/10/29 20:30]
rlu45
main:bgqprocessasampleset [2019/01/09 21:05] (current)
rlu45
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 ====== Process a sample set ====== ====== Process a sample set ======
  
-After creating ​a sample set, you can process it by selecting ​it in the sample set tree and clicking ​the ‘Process sample set’ menu item under the ‘Run’ menu.+To process ​a sample set and perform dose estimationselect ​it in the left tree and click the ‘Process sample set’ menu item under the ‘Run’ menu. The sample set can either belong to a scenario or be isolated.
  
 ===== Prepare ===== ===== Prepare =====
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 {{ file:​bgq:​process_a_sample_set_prepare.png?​nolink }} {{ file:​bgq:​process_a_sample_set_prepare.png?​nolink }}
  
-First, you need to set the value of the parameter ‘Number of blocks’, which is required ​by submission ​of one BGQ job. The recommended value is the prepopulated 1Optionally, you can also choose to simultaneously estimate radiation doses that the samples were exposed to while processing ​the sample setby selecting a calibration ​curve on the BGQ server with the ‘Select’ ​button. ​+First, you need to upload ​the calibration curves and image selection models that will be used for dose estimation on the sample set from your local computer to the server, which can be accomplished ​by the bottom area of the right panelIn the bottom areathe left tree shows the contents on the computer ​you are using; ​the right tree shows the contents in your BGQ account. In the left treelocate and select the calibration ​curves and image selection models; in the right tree, select a destination directory to which the files will be uploaded, then click the middle '​Upload' ​button. The recommended destination directory '​CalibrationCurves'​ is selected and expanded by default.
  
-Upon selection ​of curve, the image selection model associated with the curve will be automatically ​displayed in the ‘Image selection model’ text field. ​You can also use the ‘Change’ button to change ​the model that is associated ​with the curve. ​Use the bottom area of the right panel to first upload ​the curves and models.+<WRAP group> 
 +<WRAP half column>​ 
 +Then you need to set the value of the parameter ‘Number of blocks’, which is required by submission of one BGQ job. The recommended value is the prepopulated '​1'​. Optionally, you can also choose to simultaneously estimate radiation doses that the samples were exposed to while processing the sample set, by selecting one or more calibration curves on the BGQ server using the ‘Select’ button. After clicking this button, the popped-up remote file chooser will only show the curve files on the serverand the recommended '​CalibrationCurves'​ directory will also be automatically selected and expanded. 
 + 
 +The selected curve files will be filled into the drop-down list, and the image selection model associated with the curve currently being selected in the drop-down list will be displayed in the ‘Image selection model’ text field. ​Selection of another curve will result in an update of the ‘Image selection model’ text field. After initially uploading ​the curve and selection ​model files, presumably the curve file is incorrect in that the contained path to the associated ​image selection model is still for the local computer instead of the server. In this case, the software will immediately pop up a prompt dialog to tell you to correct the wrong curves; if you select a wrong curve file in the drop-down list, a similar information dialog will also appear and the background color of the ‘Image selection model’ text field will become redCorrecting ​the curve files can be accomplished using the '​Change'​ button; clicking it will result in the appearance ​of a file chooser dialog that only shows the image selection model files on the server, allowing you to select ​the correct model that the curve should use. 
 +</​WRAP>​ 
 +<WRAP half column>​ 
 +{{ file:​bgq:​remote_file_chooser_curves.png?​nolink }} 
 +</​WRAP>​ 
 +</​WRAP>​ 
 + 
 +{{ file:​bgq:​process_a_sample_set_correct_models.png?nolink }}
  
 ===== Monitor progress ===== ===== Monitor progress =====
  
-After setting ​these information,​ click the ‘Run’ button to submit jobs and start the processing of the sample set. progress dialog will appear.+After providing ​these input information,​ click the ‘Run’ button to submit jobs and start the processing of the sample set. If there are still calibration curves that have wrong paths to the associated image selection models, a dialog will pop up to prompt you to correct these curves. Otherwise a progress dialog will appear ​for the preparatory process of submitting jobs to the server, before the following dialog to monitor job progress shows up.
  
 <WRAP group> <WRAP group>
 <WRAP half column> <WRAP half column>
-In this dialog, the top grouping box displays the detailed progress information for the particular job currently being selected in the drop-down list, with the progress bar graphically showing the percentage progress of this job. +In this monitoring ​dialog, the top grouping box displays the detailed progress information for the particular job currently being selected in the drop-down list, with the progress bar graphically showing the percentage progress of this job. 
-  * ‘Status’ label: the current status of the job, among three possible ​statuses ​(Queued, Running, Finished).+  * ‘Status’ label: the current status of the job, among three possible ​states ​(Queued, Running, Finished).
   * ‘Elapsed time’ label: how long the job has been running for.   * ‘Elapsed time’ label: how long the job has been running for.
   * ‘Completed samples’ label: the number of completed samples in this job to date/the total number of samples in this job.   * ‘Completed samples’ label: the number of completed samples in this job to date/the total number of samples in this job.
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 </​WRAP>​ </​WRAP>​
 </​WRAP>​ </​WRAP>​
-  * ‘Total elapsed time’ label: how long all jobs have been running for since the first one started running. 
-  * ‘Total completed samples’ label: the number of completed samples in all jobs to date / the number of samples in this sample set. 
-  * ‘Total completed images’ label: the number of completed samples in all jobs to date / the number of images in this sample set. 
- 
  
 {{ file:​bgq:​process_a_sample_set_progress_2.png?​nolink }} {{ file:​bgq:​process_a_sample_set_progress_2.png?​nolink }}
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 <WRAP group> <WRAP group>
 <WRAP half column> <WRAP half column>
 +  * ‘Total elapsed time’ label: how long all jobs have been running for since the first one started running.
 +  * ‘Total completed samples’ label: the number of completed samples in all jobs to date / the number of samples in this sample set.
 +  * ‘Total completed images’ label: the number of completed samples in all jobs to date / the number of images in this sample set.
 +
 The text area displays a feedback message when each job terminates and a summary message after all jobs terminate. At the bottom of this dialog, four buttons provide the following functionalities:​ The text area displays a feedback message when each job terminates and a summary message after all jobs terminate. At the bottom of this dialog, four buttons provide the following functionalities:​
   * ‘Show/​Hide completed samples’ button: shows or hides the panel to the right that lists the names of all completed samples to date.   * ‘Show/​Hide completed samples’ button: shows or hides the panel to the right that lists the names of all completed samples to date.
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 </​WRAP>​ </​WRAP>​
  
 +===== Download result matrices of samples in a processed sample set =====
  
 +After finishing processing a sample set, you can download the result matrices of the contained samples to your local computer, then you can open them and perform further processing in the desktop ADCI software (e.g. estimating doses using additional calibration curves). To do this, first click the processed sample set in the scenario tree, then click the '​Download result matrices'​ menu item under the '​Run'​ menu. In the appearing file chooser dialog, select a destination directory on your local computer.
main/bgqprocessasampleset.1540845019.txt.gz · Last modified: 2018/10/29 20:30 by rlu45