ADCI Wiki

User Tools

Site Tools

Trace:
main:bgqcreateasampleforaperson

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision 		Previous revision
main:bgqcreateasampleforaperson [2018/10/29 19:34]
rlu45 		main:bgqcreateasampleforaperson [2021/02/09 16:28]
bshirley removed
Line 1: Line 1:
 ====== Create a sample for a person ====== ====== Create a sample for a person ======
  
-A sample is a compressed file of the .tgz (.tar.gzip) format, containing a number of metaphase images from the person. It is the basic unit for estimating the radiation dose that the person is exposed to. To create a sample, click the ‘New sample’ menu item within the ‘Sample sets’ menu.+A sample is a compressed file of the .tgz (.tar.gzip) format, containing a number of metaphase images from the person. It is the basic unit for estimating the radiation dose that the person was exposed to. To create a sample, click the ‘New samples’ menu item within the ‘Sample sets’ menu.
  
 ===== Prepare ===== ===== Prepare =====
Line 7: Line 7:
 {{ file:bgq:create_a_sample_prepare.png?nolink }} {{ file:bgq:create_a_sample_prepare.png?nolink }}
  
-First, you need to upload the metaphase images of the person to the BGQ server, which can be accomplished by the bottom region of the right panel. In this region, the left part displays the contents on the disk drives of the local computer you are using; the right part displays the contents on the BGQ server. In the left part, select the metaphase images or the directory containing them; in the right part, select the destination directory on the BGQ server. Then click the ‘Upload’ button in the middle. If the upload takes some time, a progress dialog will pop up. It displays the current uploading percentage in a progress bar and the name of the file being uploaded.  +<WRAP group> 
-In the right part, you can also create a new directory, rename a directory/file and delete a directory/file on the BGQ server by right-clicking on the item. You can upload multiple files and directories at one time. The metaphase images of each person should be uploaded to a separate destination directory; for example, Persons ‘S01’ and ‘S02’ will correspond to two directories on the BGQ server named ‘S01’ and ‘S02’. And the directory should only contain the images.+<WRAP half column> 
 +First, you need to upload the metaphase images of the person to the BGQ server, which can be accomplished by the bottom area of the right panel. In this area, the left part displays the contents on the disk drives of the local computer you are using; the right part displays the contents in your account on the BGQ server. In the left part, select the metaphase images or the directory containing them; in the right part, select the destination directory on the BGQ server. The default, recommended destination directory is 'MetaphaseImages', as shown in the above figure, which is automatically selected and expanded. Then click the ‘Upload’ button in the middle. If the upload takes some time, a progress dialog will pop up. It displays the current uploading percentage in a progress bar and the name of the file being uploaded. 
 +</WRAP> 
 +<WRAP half column> 
 +{{ file:bgq:upload.png?nolink }} 
 +</WRAP> 
 +</WRAP> 
 +In the right part, you can also create a new directory, rename and delete a directory/file on the BGQ server by right-clicking on the item. You can upload multiple files and directories at one time. The metaphase images of each person should be uploaded to a separate destination directory; for example, Persons ‘S01’ and ‘S02’ will correspond to two directories on the BGQ server named ‘S01’ and ‘S02’. And the directory should only contain the images.
  
-After uploading the metaphase images, you can create samples with the top region of the right panel.  You can create multiple samples at one time. Click the ‘Select’ button within the row containing the ‘Source’ label. In the directory chooser that pops up, select one or more directories to which the images were uploaded on the BGQ server, and click the ‘OK’ button.+After uploading the metaphase images, you can create samples using the top area of the right panel.  You can create multiple samples at one time. Click the ‘Select’ button within the row containing the ‘Source’ label. In the directory chooser that pops up, select one or more directories to which the images were uploaded on the BGQ server, and click the ‘OK’ button.
  
-Then the paths of all selected directories will be displayed in the drop-down list. For the source directory currently being displayed in the drop-down list, the other components in the top region of the right panel provide the following associated information:+{{ file:bgq:remote_directory_chooser.png?nolink }} 
 + 
 +Then the paths of all selected directories will be displayed in the drop-down list. For the source directory currently being selected in the drop-down list, the other components in the top area of the right panel provide the following associated information:
   * ‘Name’ text field: the name of the newly created sample. It is prepopulated with the name of the directory.   * ‘Name’ text field: the name of the newly created sample. It is prepopulated with the name of the directory.
   * ‘Description’ text area: providing a number of description entries for the sample. It is prepopulated with common entries, including ‘Coordinate of the person’ and ‘Exposed physical dose’. You can add or remove any description entry.    * ‘Description’ text area: providing a number of description entries for the sample. It is prepopulated with common entries, including ‘Coordinate of the person’ and ‘Exposed physical dose’. You can add or remove any description entry. 
Line 20: Line 29:
 You can select another directory in the drop-down list, then the ‘Name’ text field, ‘Description’ text area and ‘Metaphase images included’ list will be updated accordingly. After you finish editing ‘Name’ or ‘Description’ for one sample, its content will be automatically saved. You can also click the ‘Clear’ button to clear the contents in all of the components. Each sample must have a name, but may not have any description. You can select another directory in the drop-down list, then the ‘Name’ text field, ‘Description’ text area and ‘Metaphase images included’ list will be updated accordingly. After you finish editing ‘Name’ or ‘Description’ for one sample, its content will be automatically saved. You can also click the ‘Clear’ button to clear the contents in all of the components. Each sample must have a name, but may not have any description.
  
-===== Monitor progress =====+Then select a destination directory into which the created samples will be put by clicking the 'Select' button. This directory is also the directory from which you will create a sample set (see the next section). In the directory chooser dialog that pops up, the default directory 'SampleSets' is automatically selected and expanded. It is recommended that you right click on it, then create a new subdirectory as the destination directory. 
 + 
 +{{ file:bgq:remote_directory_chooser_new_samples_desti.png?nolink }} 
 + 
 +===== Download metaphase images from an external computer =====
  
 <WRAP group> <WRAP group>
 <WRAP half column> <WRAP half column>
 +It is very likely that metaphase images are produced by microscope devices of a remote laboratory, thus initially stored on a remote computer of the laboratory. In this case, the images need to be first downloaded to the local computer that you are using, which can also be accomplished by the bottom area of the right panel. In the drop-down list in the right part of the panel, select the item 'Connect to another computer'. In the popped-up dialog, enter the IP address or host name of the remote computer from which you want to download metaphase images, the port number, the user name of an account on that computer and the corresponding password. The remote computer you want to connect to must be running an SSH server.
 +
 +The following figure shows that after successfully connecting to the remote computer, its name will be filled into the drop-down list and selected. For privacy, the right tree will only show the contents in one directory on the remote computer, which is the 'Biodosimetry' subdirectory under the default directory (on the Windows operating system, the default directory is (System drive):/Users/(User name)). Therefore, in order to be able to see the metaphase image files, they need to be first placed under the 'Biodosimetry' subdirectory on the remote computer.
 +</WRAP>
 +<WRAP half column>
 +{{ file:bgq:connect_to_remote_computer.png?nolink }}
 +</WRAP>
 +</WRAP>
 +
 +{{ file:bgq:remote_computer.png?nolink }}
 +
 +===== Monitor progress =====
 +
 After finishing entering these preparation information, the process of creating samples from the source directories can be started by clicking the ‘Create’ button. If a source directory contains other files besides the *.tif images, those files will be first deleted. Then a progress dialog will pop up. After finishing entering these preparation information, the process of creating samples from the source directories can be started by clicking the ‘Create’ button. If a source directory contains other files besides the *.tif images, those files will be first deleted. Then a progress dialog will pop up.
  
 +<WRAP group>
 +<WRAP half column>
 In the top grouping box of this progress dialog, the progress bar displays the percentage progress of creating the sample currently being selected in the drop-down list. The components n the middle grouping box display the following information: In the top grouping box of this progress dialog, the progress bar displays the percentage progress of creating the sample currently being selected in the drop-down list. The components n the middle grouping box display the following information:
   * ‘Completed samples’ label: displays the number of samples that have finished creating to date / the total number of samples.   * ‘Completed samples’ label: displays the number of samples that have finished creating to date / the total number of samples.
Line 36: Line 64:
 </WRAP> </WRAP>
 <WRAP half column> <WRAP half column>
-{{ file:dialog:create_a_sample_progress.png?nolink }}+{{ file:bgq:create_a_sample_progress.png?nolink }}
 </WRAP> </WRAP>
 </WRAP> </WRAP>
  

Page Tools

Donate Powered by PHP Valid HTML5 Valid CSS Driven by DokuWiki