array in macro functions
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Hi,i have coordinates of hundreds of irregularly shaped polygons that i want to draw on a single image. I do not have the polygons as ROIs, unfortunately. I want to usea list of coordinates from another software. I managed to import them in an array, but when i wanted to use makePolygon(coord); where coord is an array of all the coordinates of a polygon, i got the failure message: Numer or numeric function is required. When i wrote a list of coordinates one by one in the makePolygon function it worked well, but I do not have the time to write all the many thousand coordinates of many hundred polygons that way.
How can I use list of coordinates for making polygons? Many thank in advance!Csaba -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Dear Csaba,
You need something like: coord = newArray(20,48,59,13,101,40,75,77,38,70); makePolygon(coord[0],coord[1],coord[2],coord[3],coord[4],coord[5],coord[6],coord[7],coord[8],coord[9]); I guess it depends a little how many sides your polygons will have how to implement this. Best wishes Kees Dr Ir K.R. Straatman Senior Experimental Officer Advanced Imaging Facility Centre for Core Biotechnology Services University of Leicester www.le.ac.uk/advanced-imaging-facility -----Original Message----- From: Csaba DÁVID [mailto:[hidden email]] Sent: 15 February 2018 20:28 To: [hidden email] Subject: array in macro functions Hi,i have coordinates of hundreds of irregularly shaped polygons that i want to draw on a single image. I do not have the polygons as ROIs, unfortunately. I want to usea list of coordinates from another software. I managed to import them in an array, but when i wanted to use makePolygon(coord); where coord is an array of all the coordinates of a polygon, i got the failure message: Numer or numeric function is required. When i wrote a list of coordinates one by one in the makePolygon function it worked well, but I do not have the time to write all the many thousand coordinates of many hundred polygons that way. How can I use list of coordinates for making polygons? Many thank in advance!Csaba -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Dear Kees,this is exactly what I wanted to avoid, since each of the polygons have different number of points, so I cannot express them in a general format. Is there any tricky way? Maybe?Best regardsCsaba
On Friday, February 16, 2018 9:55 AM, "Straatman, Kees (Dr.)" <[hidden email]> wrote: Dear Csaba, You need something like: coord = newArray(20,48,59,13,101,40,75,77,38,70); makePolygon(coord[0],coord[1],coord[2],coord[3],coord[4],coord[5],coord[6],coord[7],coord[8],coord[9]); I guess it depends a little how many sides your polygons will have how to implement this. Best wishes Kees Dr Ir K.R. Straatman Senior Experimental Officer Advanced Imaging Facility Centre for Core Biotechnology Services University of Leicester www.le.ac.uk/advanced-imaging-facility -----Original Message----- From: Csaba DÁVID [mailto:[hidden email]] Sent: 15 February 2018 20:28 To: [hidden email] Subject: array in macro functions Hi,i have coordinates of hundreds of irregularly shaped polygons that i want to draw on a single image. I do not have the polygons as ROIs, unfortunately. I want to usea list of coordinates from another software. I managed to import them in an array, but when i wanted to use makePolygon(coord); where coord is an array of all the coordinates of a polygon, i got the failure message: Numer or numeric function is required. When i wrote a list of coordinates one by one in the makePolygon function it worked well, but I do not have the time to write all the many thousand coordinates of many hundred polygons that way. How can I use list of coordinates for making polygons? Many thank in advance!Csaba -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Dear Csaba,
I recommend to switch to some of the more powerful scripting languages [1], e.g. Groovy, Javascript, Beanshell or Jython. They provide syntactic constructs (such as list comprehensions) that facilitate this kind of task. In addition, you have full access to the underlying Java API [2] to create your Roi objects. Cheers Jan [1]: https://imagej.net/Scripting#Supported_languages [2]: http://javadoc.scijava.org/ImageJ1/index.html?overview-summary.html On 16.02.2018 10:09, Csaba DÁVID wrote: > Dear Kees,this is exactly what I wanted to avoid, since each of the polygons have different number of points, so I cannot express them in a general format. Is there any tricky way? Maybe?Best regardsCsaba > > On Friday, February 16, 2018 9:55 AM, "Straatman, Kees (Dr.)" <[hidden email]> wrote: > > > Dear Csaba, > > You need something like: > > coord = newArray(20,48,59,13,101,40,75,77,38,70); > makePolygon(coord[0],coord[1],coord[2],coord[3],coord[4],coord[5],coord[6],coord[7],coord[8],coord[9]); > > I guess it depends a little how many sides your polygons will have how to implement this. > > Best wishes > > Kees > > > Dr Ir K.R. Straatman > Senior Experimental Officer > Advanced Imaging Facility > Centre for Core Biotechnology Services > University of Leicester > www.le.ac.uk/advanced-imaging-facility > > > > -----Original Message----- > From: Csaba DÁVID [mailto:[hidden email]] > Sent: 15 February 2018 20:28 > To: [hidden email] > Subject: array in macro functions > > Hi,i have coordinates of hundreds of irregularly shaped polygons that i want to draw on a single image. I do not have the polygons as ROIs, unfortunately. I want to usea list of coordinates from another software. I managed to import them in an array, but when i wanted to use makePolygon(coord); where coord is an array of all the coordinates of a polygon, i got the failure message: Numer or numeric function is required. When i wrote a list of coordinates one by one in the makePolygon function it worked well, but I do not have the time to write all the many thousand coordinates of many hundred polygons that way. > How can I use list of coordinates for making polygons? > Many thank in advance!Csaba > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Dear Jan,thank you for your advice. I was afraid that I have to learn another language. But it is probably not possible to learn Java in a week :(
ThanksCsaba On Friday, February 16, 2018 10:25 AM, Jan Eglinger <[hidden email]> wrote: Dear Csaba, I recommend to switch to some of the more powerful scripting languages [1], e.g. Groovy, Javascript, Beanshell or Jython. They provide syntactic constructs (such as list comprehensions) that facilitate this kind of task. In addition, you have full access to the underlying Java API [2] to create your Roi objects. Cheers Jan [1]: https://imagej.net/Scripting#Supported_languages [2]: http://javadoc.scijava.org/ImageJ1/index.html?overview-summary.html On 16.02.2018 10:09, Csaba DÁVID wrote: > Dear Kees,this is exactly what I wanted to avoid, since each of the polygons have different number of points, so I cannot express them in a general format. Is there any tricky way? Maybe?Best regardsCsaba > > On Friday, February 16, 2018 9:55 AM, "Straatman, Kees (Dr.)" <[hidden email]> wrote: > > > Dear Csaba, > > You need something like: > > coord = newArray(20,48,59,13,101,40,75,77,38,70); > makePolygon(coord[0],coord[1],coord[2],coord[3],coord[4],coord[5],coord[6],coord[7],coord[8],coord[9]); > > I guess it depends a little how many sides your polygons will have how to implement this. > > Best wishes > > Kees > > > Dr Ir K.R. Straatman > Senior Experimental Officer > Advanced Imaging Facility > Centre for Core Biotechnology Services > University of Leicester > www.le.ac.uk/advanced-imaging-facility > > > > -----Original Message----- > From: Csaba DÁVID [mailto:[hidden email]] > Sent: 15 February 2018 20:28 > To: [hidden email] > Subject: array in macro functions > > Hi,i have coordinates of hundreds of irregularly shaped polygons that i want to draw on a single image. I do not have the polygons as ROIs, unfortunately. I want to usea list of coordinates from another software. I managed to import them in an array, but when i wanted to use makePolygon(coord); where coord is an array of all the coordinates of a polygon, i got the failure message: Numer or numeric function is required. When i wrote a list of coordinates one by one in the makePolygon function it worked well, but I do not have the time to write all the many thousand coordinates of many hundred polygons that way. > How can I use list of coordinates for making polygons? > Many thank in advance!Csaba > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by Jan Eglinger
Good day,
did you consider: "*makeSelection(type, xcoord, ycoord)* Creates a selection from a list of XY coordinates. The first argument should be "polygon", "freehand", "polyline", "freeline", "angle" or "point", or the numeric value returned by selectionType. The xcoord and ycoord arguments are numeric arrays that contain the X and Y coordinates. See the MakeSelectionDemo macro for examples." Regards Herbie :::::::::::::::::::::::::::::::::::::::::: Am 16.02.18 um 10:23 schrieb Jan Eglinger: > Dear Csaba, > > I recommend to switch to some of the more powerful scripting languages > [1], e.g. Groovy, Javascript, Beanshell or Jython. > They provide syntactic constructs (such as list comprehensions) that > facilitate this kind of task. In addition, you have full access to the > underlying Java API [2] to create your Roi objects. > > Cheers > Jan > > [1]: https://imagej.net/Scripting#Supported_languages > [2]: http://javadoc.scijava.org/ImageJ1/index.html?overview-summary.html > > On 16.02.2018 10:09, Csaba DÁVID wrote: >> Dear Kees,this is exactly what I wanted to avoid, since each of the >> polygons have different number of points, so I cannot express them in >> a general format. Is there any tricky way? Maybe?Best regardsCsaba >> >> On Friday, February 16, 2018 9:55 AM, "Straatman, Kees (Dr.)" >> <[hidden email]> wrote: >> >> Dear Csaba, >> >> You need something like: >> >> coord = newArray(20,48,59,13,101,40,75,77,38,70); >> makePolygon(coord[0],coord[1],coord[2],coord[3],coord[4],coord[5],coord[6],coord[7],coord[8],coord[9]); >> >> >> I guess it depends a little how many sides your polygons will have how >> to implement this. >> >> Best wishes >> >> Kees >> >> >> Dr Ir K.R. Straatman >> Senior Experimental Officer >> Advanced Imaging Facility >> Centre for Core Biotechnology Services >> University of Leicester >> www.le.ac.uk/advanced-imaging-facility >> >> >> >> -----Original Message----- >> From: Csaba DÁVID [mailto:[hidden email]] >> Sent: 15 February 2018 20:28 >> To: [hidden email] >> Subject: array in macro functions >> >> Hi,i have coordinates of hundreds of irregularly shaped polygons that >> i want to draw on a single image. I do not have the polygons as ROIs, >> unfortunately. I want to usea list of coordinates from another >> software. I managed to import them in an array, but when i wanted to >> use makePolygon(coord); where coord is an array of all the coordinates >> of a polygon, i got the failure message: Numer or numeric function is >> required. When i wrote a list of coordinates one by one in the >> makePolygon function it worked well, but I do not have the time to >> write all the many thousand coordinates of many hundred polygons that >> way. >> How can I use list of coordinates for making polygons? >> Many thank in advance!Csaba >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> >> >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by Csaba DÁVID
On Friday, 16 February 2018 09:31:50 GMT Csaba DÁVID wrote:
> Dear Jan,thank you for your advice. I was afraid that I have to learn > another language. But it is probably not possible to learn Java in a week > :( ThanksCsaba You do not have to learn another language if you can do this as a macro: You need to have stored the list of coordinates in some file or a text, so you have one ROI per line. Read the file somehow (there are macros showing how to do that in the examples). Then, make a loop: Read one line of the text file (ROI) at a time, Parse the number of coordinates in that line (there is a split function in the macro language), and count them, e.g. 15. Create the x and y arrays with that number of items coorx=newArray(15), etc. Assign the coordinates to the array (you can use another loop) Call the makeSelection function as Herbie suggested Plot the ROI End of loop. In the macro language you can generate an array again with a different number of items at each iteration of the loop. You cannot do that in Java without resorting to some tricks or using a List. Hope it helps. Gabriel -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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