Batch mode and Results window
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Batch mode and Results window
 
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Hi all,
I need to open images in a folder and their matching files of multiple ROIs coordinates (several hundreds per image) to perform measurements. A single macro works fine, but using setbatchmode(true) to make it faster, I do not get any Results window, and therefore I can´t access measurements. I have tried to place setbatchmode("show") or setbatchmode(true) at different places in the loop without success. Is this normal? No access to Results window if setbatchmode is enabled? My macro follows: setBatchMode(true); run("Set Measurements...", "mean redirect=None decimal=2"); //listaArchivos is an array containing my list of files for (i = 0; i<listaArchivos.length;i++) { open(carpetaROIs + File.separator + ROIs[i]); //carpetaROIs and ROIs are the folder and the list of archive for the rois open(carpeta + File.separator + listaArchivos[i]); carpeta and listaArchivos are the folder and the list of images roiManager("Measure"); close("ROI Manager"); close("*"); } saveAs("Results", carpeta + File.separator + ROIs[i] + "_Histogra" + ".txt"); -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Dear Pedro,
I would say that is not normal. In batchmode you should get a results table, see macro code below. setBatchMode(true); run("Blobs (25K)"); setAutoThreshold("Default"); setOption("BlackBackground", false); run("Convert to Mask"); run("Analyze Particles...", "add"); roiManager("Measure"); Is it possible that you close the ROI Manager before the measurements are finished? What happens if you run the macro till roiManager("Measure"); ? Best wishes Kees -----Original Message----- Sent: 04 May 2021 09:53 Subject: Batch mode and Results window Hi all, I need to open images in a folder and their matching files of multiple ROIs coordinates (several hundreds per image) to perform measurements. A single macro works fine, but using setbatchmode(true) to make it faster, I do not get any Results window, and therefore I can´t access measurements. I have tried to place setbatchmode("show") or setbatchmode(true) at different places in the loop without success. Is this normal? No access to Results window if setbatchmode is enabled? My macro follows: setBatchMode(true); run("Set Measurements...", "mean redirect=None decimal=2"); //listaArchivos is an array containing my list of files for (i = 0; i<listaArchivos.length;i++) { open(carpetaROIs + File.separator + ROIs[i]); //carpetaROIs and ROIs are the folder and the list of archive for the rois open(carpeta + File.separator + listaArchivos[i]); carpeta and listaArchivos are the folder and the list of images roiManager("Measure"); close("ROI Manager"); close("*"); } saveAs("Results", carpeta + File.separator + ROIs[i] + "_Histogra" + ".txt"); -- ImageJ mailing list: https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimagej.nih.gov%2Fij%2Flist.html&data=04%7C01%7Ckrs5%40leicester.ac.uk%7C275753dca9be4ece88f108d90edb8d79%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C1%7C637557158401961910%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=UAm%2Bjk2Fau01b2u0Pj7wkSrfWE%2Bpf0XkbNA2GOxg3zg%3D&reserved=0 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Besides that, I think you want to have your saveAs command within the loop
Kees -----Original Message----- Sent: 04 May 2021 12:12 Subject: Re: Batch mode and Results window Dear Pedro, I would say that is not normal. In batchmode you should get a results table, see macro code below. setBatchMode(true); run("Blobs (25K)"); setAutoThreshold("Default"); setOption("BlackBackground", false); run("Convert to Mask"); run("Analyze Particles...", "add"); roiManager("Measure"); Is it possible that you close the ROI Manager before the measurements are finished? What happens if you run the macro till roiManager("Measure"); ? Best wishes Kees -----Original Message----- Sent: 04 May 2021 09:53 Subject: Batch mode and Results window Hi all, I need to open images in a folder and their matching files of multiple ROIs coordinates (several hundreds per image) to perform measurements. A single macro works fine, but using setbatchmode(true) to make it faster, I do not get any Results window, and therefore I can´t access measurements. I have tried to place setbatchmode("show") or setbatchmode(true) at different places in the loop without success. Is this normal? No access to Results window if setbatchmode is enabled? My macro follows: setBatchMode(true); run("Set Measurements...", "mean redirect=None decimal=2"); //listaArchivos is an array containing my list of files for (i = 0; i<listaArchivos.length;i++) { open(carpetaROIs + File.separator + ROIs[i]); //carpetaROIs and ROIs are the folder and the list of archive for the rois open(carpeta + File.separator + listaArchivos[i]); carpeta and listaArchivos are the folder and the list of images roiManager("Measure"); close("ROI Manager"); close("*"); } saveAs("Results", carpeta + File.separator + ROIs[i] + "_Histogra" + ".txt"); -- ImageJ mailing list: https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimagej.nih.gov%2Fij%2Flist.html&data=04%7C01%7Ckrs5%40leicester.ac.uk%7C5123c25a890c4b832ff608d90eed9b6c%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C1%7C637557235947403697%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=migEWiPHmkMkSbSrazBDzTJiZqU4zViO6WGouktYuwE%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%7Ckrs5%40leicester.ac.uk%7C5123c25a890c4b832ff608d90eed9b6c%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C1%7C637557235947403697%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=migEWiPHmkMkSbSrazBDzTJiZqU4zViO6WGouktYuwE%3D&reserved=0 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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