JACoP Batch Processing
Locked
 
|
Hello,
I am currently running colocalization analysis using the JACoP plugin and have built a macro to automate this process. After attempting to make it generic, I keep receiving an error message when attempting to run the macro. I am hoping someone can spot the error and help me fix it. I have pasted the macro as well as the error message I am receiving below. Error: ')' expected in line 13: run ( "JACoP " , "imga=[" <C1> - "+img_name] imgb=[" C2 - "+img_name] thra=4500 thrb=6500 pearson mm costesthr costesra... img_name=getTitle(); run("Next Slice [>]"); run("Next Slice [>]"); run("Delete Slice", "delete=channel"); run("Split Channels"); selectWindow("C1-"+img_name); selectWindow("C2-"+img_name); selectWindow("C1-"+img_name); selectWindow("C2-"+img_name); run("JACoP "); selectWindow("C1-"+img_name); selectWindow("C2-"+img_name); run("JACoP ", "imga=["C1-"+img_name] imgb=["C2-"+img_name] thra=4500 thrb=6500 pearson mm costesthr costesrand=2-1-200-0.001-0-false-true-true"); selectWindow("Costes' threshold ["C1-"+img_name] and ["C2-"+img_name]"); selectWindow("Costes' mask"); selectWindow("Randomized images of ["C2-"+img_name]"); selectWindow("Costes' method (["C1-"+img_name] & ["C2-"+img_name])"); selectWindow("Costes' threshold ["C1-"+img_name] and ["C2-"+img_name]"); selectWindow("Costes' mask"); selectWindow("Randomized images of ["C2-"+img_name]"); selectWindow("Costes' method (["C1-"+img_name] & ["C2-"+img_name])"); selectWindow("C1-"+img_name); selectWindow("C2-"+img_name); selectWindow("C1-"+img_name); selectWindow("C2-"+img_name); saveAs("Text", "/Volumes/ALEXIUS_D/Flourescent Microscopy/DENV2_100xmag/Output/Log.txt"); close(); selectWindow("C1-"+img_name); selectWindow("C2-"+img_name); selectWindow("Costes' mask"); close(); selectWindow("C1-"+img_name); selectWindow("C2-"+img_name); selectWindow("Randomized images of ["C2-"+img_name]"); close(); selectWindow("C1-"+img_name); selectWindow("C2-"+img_name); selectWindow("Costes' method (["C1-"+img_name] & ["C2-"+img_name])"); close(); selectWindow("C1-"+img_name); selectWindow("C2-"+img_name); selectWindow("C1-"+img_name); close(); selectWindow("C2-"+img_name); close(); -- Sent from: http://imagej.1557.x6.nabble.com/ -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
|
|
Hi Adingle,
You may need to escape the quotes inside strings: run ( "JACoP " , "imga=[" <C1> - "+img_name] imgb=[" C2 - "+img_name] ... try changing to: run ( "JACoP " , "imga=[\" <C1> - \"+img_name] imgb=[\" C2 - \"+img_name] The second argument assigns a concatenated string to imga and that has quotes that will terminate the argument string unless escaped. I am not certain this is the issue -- I am not familiar with the JACoP call syntax -- but it would explain the error message. Best wishes, Mark Mark Chopping, Ph.D. (he, him, his) <--what's this? <https://www.glsen.org/activity/pronouns-guide-glsen> Director, Ph.D. Program in Environmental Science and Management Professor, Department of Earth and Environmental Studies Montclair State University, Montclair, NJ 07043 Tel. (973) 655-7384 Fax: (973) 655-4072 https://www.montclair.edu/environmental-management-phd http://www.montclair.edu/csam/remote-sensing-lab <https://www.montclair.edu> [image: above.nasa.gov] <http://above.nasa.gov> <https://www.majortaylorclub.com/> <https://misr.jpl.nasa.gov/> All opinions expressed here are my own and do not represent the views or policies of Montclair State University, NASA, NJ DEP, NACP, USDA, MTCCNJ, or AGU. On Thu, Mar 25, 2021 at 9:55 PM Adingle <[hidden email]> wrote: > Hello, > > I am currently running colocalization analysis using the JACoP plugin and > have built a macro to automate this process. After attempting to make it > generic, I keep receiving an error message when attempting to run the > macro. > I am hoping someone can spot the error and help me fix it. I have pasted > the > macro as well as the error message I am receiving below. > > Error: ')' expected in line 13: > > run ( "JACoP " , "imga=[" <C1> - "+img_name] imgb=[" C2 - "+img_name] > thra=4500 thrb=6500 pearson mm costesthr costesra... > > > img_name=getTitle(); > run("Next Slice [>]"); > run("Next Slice [>]"); > run("Delete Slice", "delete=channel"); > run("Split Channels"); > selectWindow("C1-"+img_name); > selectWindow("C2-"+img_name); > selectWindow("C1-"+img_name); > selectWindow("C2-"+img_name); > run("JACoP "); > selectWindow("C1-"+img_name); > selectWindow("C2-"+img_name); > run("JACoP ", "imga=["C1-"+img_name] imgb=["C2-"+img_name] thra=4500 > thrb=6500 pearson mm costesthr > costesrand=2-1-200-0.001-0-false-true-true"); > selectWindow("Costes' threshold ["C1-"+img_name] and ["C2-"+img_name]"); > selectWindow("Costes' mask"); > selectWindow("Randomized images of ["C2-"+img_name]"); > selectWindow("Costes' method (["C1-"+img_name] & ["C2-"+img_name])"); > selectWindow("Costes' threshold ["C1-"+img_name] and ["C2-"+img_name]"); > selectWindow("Costes' mask"); > selectWindow("Randomized images of ["C2-"+img_name]"); > selectWindow("Costes' method (["C1-"+img_name] & ["C2-"+img_name])"); > selectWindow("C1-"+img_name); > selectWindow("C2-"+img_name); > selectWindow("C1-"+img_name); > selectWindow("C2-"+img_name); > > saveAs("Text", "/Volumes/ALEXIUS_D/Flourescent > Microscopy/DENV2_100xmag/Output/Log.txt"); > close(); > selectWindow("C1-"+img_name); > selectWindow("C2-"+img_name); > selectWindow("Costes' mask"); > close(); > selectWindow("C1-"+img_name); > selectWindow("C2-"+img_name); > selectWindow("Randomized images of ["C2-"+img_name]"); > close(); > selectWindow("C1-"+img_name); > selectWindow("C2-"+img_name); > selectWindow("Costes' method (["C1-"+img_name] & ["C2-"+img_name])"); > close(); > selectWindow("C1-"+img_name); > selectWindow("C2-"+img_name); > selectWindow("C1-"+img_name); > close(); > selectWindow("C2-"+img_name); > close(); > > > > > -- > Sent from: http://imagej.1557.x6.nabble.com/ > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
|
|
In reply to this post by Adingle
I think you need to skip the first quote in the assignments and add +", like this:
run("JACoP ", "imga=[C1-"+img_name+"] imgb=[C2-"+img_name+"] thra=4500 thrb=6500 pearson mm costesthr costesrand=2-1-200-0.001-0-false-true-true"); A cleaner solution could perhaps be to do it this way instead: ... selectWindow("C1-"+img_name); img1 = getTitle; selectWindow("C2-"+img_name); img2 = getTitle; ... run("JACoP ", "imga=[&img1] imgb=[&img2] thra=4500 thrb=6500 pearson mm costesthr costesrand=2-1-200-0.001-0-false-true-true"); ... Stein -----Original Message----- Sent: 26. mars 2021 02:45 Subject: JACoP Batch Processing Hello, I am currently running colocalization analysis using the JACoP plugin and have built a macro to automate this process. After attempting to make it generic, I keep receiving an error message when attempting to run the macro. I am hoping someone can spot the error and help me fix it. I have pasted the macro as well as the error message I am receiving below. Error: ')' expected in line 13: run ( "JACoP " , "imga=[" <C1> - "+img_name] imgb=[" C2 - "+img_name] thra=4500 thrb=6500 pearson mm costesthr costesra... img_name=getTitle(); run("Next Slice [>]"); run("Next Slice [>]"); run("Delete Slice", "delete=channel"); run("Split Channels"); selectWindow("C1-"+img_name); selectWindow("C2-"+img_name); selectWindow("C1-"+img_name); selectWindow("C2-"+img_name); run("JACoP "); selectWindow("C1-"+img_name); selectWindow("C2-"+img_name); run("JACoP ", "imga=["C1-"+img_name] imgb=["C2-"+img_name] thra=4500 thrb=6500 pearson mm costesthr costesrand=2-1-200-0.001-0-false-true-true"); selectWindow("Costes' threshold ["C1-"+img_name] and ["C2-"+img_name]"); selectWindow("Costes' mask"); selectWindow("Randomized images of ["C2-"+img_name]"); selectWindow("Costes' method (["C1-"+img_name] & ["C2-"+img_name])"); selectWindow("Costes' threshold ["C1-"+img_name] and ["C2-"+img_name]"); selectWindow("Costes' mask"); selectWindow("Randomized images of ["C2-"+img_name]"); selectWindow("Costes' method (["C1-"+img_name] & ["C2-"+img_name])"); selectWindow("C1-"+img_name); selectWindow("C2-"+img_name); selectWindow("C1-"+img_name); selectWindow("C2-"+img_name); saveAs("Text", "/Volumes/ALEXIUS_D/Flourescent Microscopy/DENV2_100xmag/Output/Log.txt"); close(); selectWindow("C1-"+img_name); selectWindow("C2-"+img_name); selectWindow("Costes' mask"); close(); selectWindow("C1-"+img_name); selectWindow("C2-"+img_name); selectWindow("Randomized images of ["C2-"+img_name]"); close(); selectWindow("C1-"+img_name); selectWindow("C2-"+img_name); selectWindow("Costes' method (["C1-"+img_name] & ["C2-"+img_name])"); close(); selectWindow("C1-"+img_name); selectWindow("C2-"+img_name); selectWindow("C1-"+img_name); close(); selectWindow("C2-"+img_name); close(); -- Sent from: https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimagej.1557.x6.nabble.com%2F&data=04%7C01%7Cstein.rorvik%40sintef.no%7Ca776d4e8a406442e8d8108d8effa3d89%7Ce1f00f39604145b0b309e0210d8b32af%7C1%7C0%7C637523205366514571%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=MS0FGKaU6PbIWW3H%2BHTvYG0vcq5i1pO3T6HSqih17P4%3D&reserved=0 -- ImageJ mailing list: https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimagej.nih.gov%2Fij%2Flist.html&data=04%7C01%7Cstein.rorvik%40sintef.no%7Ca776d4e8a406442e8d8108d8effa3d89%7Ce1f00f39604145b0b309e0210d8b32af%7C1%7C0%7C637523205366514571%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=AlYwHICEczUaivONIZkwVR4CT5KSTNHQBXDcdBb3Npk%3D&reserved=0 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
|
|
In reply to this post by Mark Chopping
Hello Mark,
Thanks for your suggestion. I made the change but it did not work. I copied the line here for reference as well as the error message. run("JACoP ", "imga=[\"C1-\"+img_name] imgb=[\"C2-\"+img_name] thra=4500 thrb=6500 pearson mm costesthr costesrand=2-1-200-0.001-0-false-true-true"); Error: Image not found while running JACoP from a macro 1-Use "open(path)" in your macro to open images 2-Make sure you have called the right image ! in line 13: run ( "JACoP " , "imga=["C1-"+img_name] imgb=["C2-"+img_name] thra=4500 thrb=6500 pearson mm costesthr costesrand=2-1-2... -- Sent from: http://imagej.1557.x6.nabble.com/ -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
|
|
In reply to this post by Stein Rørvik
Hello Stein,
Thank you for your suggestion! It fixed the problem that I was having. I just have one more question. I'm am trying to select the Costes' Threshold window to close it out, yet I'm am receiving an error saying "No window with the title "Costes' threshold [C1-Snap-xxx.czi] and [C2-Snap-xxx.czi]" found." Do you have any suggestions to fix this as well? Here is how it is written in the macro. selectWindow("Costes' threshold [C1-"+img_name+"] and [C2-"+img_name+"]"); Alexius -- Sent from: http://imagej.1557.x6.nabble.com/ -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
|
|
Are you sure that the window's name is really "Costes' threshold [C1-Snap-xxx.czi] and [C2-Snap-xxx.czi]" ?
If it does not have this exact name, the macro will not find it. Revise the string so it matches. If all you want to do is to close the window, the command close("Costes*"); would probably be easier to use. Stein -----Original Message----- Sent: 26. mars 2021 14:52 Subject: Re: JACoP Batch Processing Hello Stein, Thank you for your suggestion! It fixed the problem that I was having. I just have one more question. I'm am trying to select the Costes' Threshold window to close it out, yet I'm am receiving an error saying "No window with the title "Costes' threshold [C1-Snap-xxx.czi] and [C2-Snap-xxx.czi]" found." Do you have any suggestions to fix this as well? Here is how it is written in the macro. selectWindow("Costes' threshold [C1-"+img_name+"] and [C2-"+img_name+"]"); Alexius -- Sent from: https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimagej.1557.x6.nabble.com%2F&data=04%7C01%7Cstein.rorvik%40sintef.no%7C44f2eb65872e4c0f90a308d8f05e65bf%7Ce1f00f39604145b0b309e0210d8b32af%7C1%7C0%7C637523635523781942%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=9YytP7G%2F8eOhPmd%2BoodWmCUVLpvtutoUbKGi5XgObz4%3D&reserved=0 -- ImageJ mailing list: https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimagej.nih.gov%2Fij%2Flist.html&data=04%7C01%7Cstein.rorvik%40sintef.no%7C44f2eb65872e4c0f90a308d8f05e65bf%7Ce1f00f39604145b0b309e0210d8b32af%7C1%7C0%7C637523635523791899%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=LJsuFHplo5s0bsvVd7ffd32nzJEULazvgjLjaOOsblY%3D&reserved=0 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
«
Return to ImageJ
|
1 view|%1 views
| Free forum by Nabble | Edit this page |