ImageJ has a nice contour plot plugin that might be downloaded from this link: http://imagej.nih.gov/ij/plugins/contour-plotter.html , it works fine and easily.
However, saving the image including the contour plot is not trivial, Using the save or save as options will save the image without the contour. It sound that the problem is in my understanding of how to merge the contour layer with the image layer.
I would be thankful if you can instruct me how to save the contour plot and the image in one file rather than taking a snapshot of the screen.
According to the source contained in Contour_Plotter.jar, the contours are drawn directly onto the Graphics object of the parent ImageCanvas:
private ImageCanvas Parent_Canvas;
private Graphics Parent_Graphics;
[...]
Parent_Graphics = Parent_Canvas.getGraphics();
[...]
Parent_Graphics.drawLine(
(int)(Parent_Canvas.screenX((int)(pts[pt_right][X]+0.5))),
(int)(Parent_Canvas.screenY((int)(pts[pt_right][Y]+0.5))),
(int)(Parent_Canvas.screenX((int)(pts[pt_at][X]+0.5))),
(int)(Parent_Canvas.screenY((int)(pts[pt_at][Y]+0.5))));
It seems that the plugin was written before ImageJ had introduced the concept of Overlays, and apparently it has not been maintained for a decade now. You can write to the ImageJ mailing list however and ask if the plugin is still maintained.
Unless you want to take a screenshot of the current image and save this, I would suggest you use a different approach using a sequence such as:
set a threshold (Image > Adjust > Threshold...)
convert it to a selection (Edit > Selection > Create Selection)
draw the contour of the selection (Edit > Draw) or add it as a new overlay (Image > Overlay > Add Selection...)
You can automate this process for various intensity levels (i.e. threshold values) using the macro recorder, see also this tutorial.
Related
I generated a table with iText7 (C#):
var cell = new Cell().Add(new Paragraph(headers[c]).SetFont(font).SetFontColor(ColorConstants.WHITE).SetFontSize(size).SetBold());
cell.SetBackgroundColor(color);
cell.SetTextAlignment(iText.Layout.Properties.TextAlignment.CENTER);
cell.SetPadding(0);
cell.SetBorder(new SolidBorder(1));
table.AddCell(cell);
Document has the table, but on certain scalings, it looks weird on the edges:
Taking a closer look on the image above:
If however I change the zoom in the viewer directly, it looks OK:
How do I get rid of these unnecessary parts from the border?
I'm attaching here the resulted PDF for reference:
Download sample PDF
I also noticed that on iText KB pages, there is this kind of behavior:
https://kb.itextpdf.com/home/it7kb/faq/how-do-i-change-the-border-color-of-a-pdfpcell
See the red and blue bars' left edges:
This behaviour is not uncommon in PDF or other print drivers where vectors are printed rather than plotter definitions (often called "Dangles". It would be worse if the definition was rounded or square, rather than butt, and join as "mitre" cannot apply, see below). The overlap is intentional (to ensure both lines are inclusive). In a laser drum print that may be desirable overkill, but disastrous for any inkjet or screen. It looks like the cell is not bordered by a box, but using common straight vectors. Again this is often desirable optimisation but not when the weight is not honoured. Thus it depends if the viewer is using the correct thickness.
All desktop PDF viewers (icluding Chrome and FireFox) I tested showed the lines correctly as clean overlap without "Dangles". Acrobat has a reputation for undesirably thickening or thinning its standard defined lines depending on its user settings.
I am considering drawing a network.
For example, as shown in the demo, we can use the dashboard to get the chart, but there is no "save button" on the right side, as is often the case.
cux_df = cuxfilter.DataFrame.load_graph((nodes, edges))
chart0 = cuxfilter.charts.dashader.graph(node_pixel_shade_type='linear', unselected_alpha=0.2)
d = cux_df.dashboard([chart0], layout=cuxfilter.layouts.double_feature)
chart0.view()
Since we are using large data, we would like to take advantage of cuxfilter's quick drawings. If holoviews, for example, it takes too long to compute. Screen captures, etc. are possible, but is there any way to save the resulting figure?
Drawing with datashader took too long. I could create a view screen with cuxfilter.
The only way right now is to use the dashboard preview() function, which screen captures the dashboard in it's initial state and saves it as a png file. The way to do that is as follows:
cux_df = cuxfilter.DataFrame.load_graph((nodes, edges))
chart0 = cuxfilter.charts.dashader.graph(node_pixel_shade_type='linear', unselected_alpha=0.2)
d = cux_df.dashboard([chart0], layout=cuxfilter.layouts.double_feature)
await d.preview()
This would only work in a jupyter lab/notebook environment though, and is restrictive in capturing current state.
Based on your suggestion, it was as easy as adding an extra tool to the chart using bokeh, so we ended up adding it as a new feature, for all the bokeh and datashader based charts, the progress can be tracked here. To try it out once the changes are merged, you would have to install the cuxfilter nightly version (23.02). Once the changes are merged, this is how the toolbar would look:
I'm currently looking for a way to create a 'configurator' for a upholsters, similar to http://digitaldraping.com/configurator/furniture-sofa/?Cushions_Plain-Cream.png,Sofa_Stripe-Orange.png - you select your fabrics and they are 'drawn' on the sofa automatically.
Unfortunately, all the sites I've looked at seem to use pre-rendered transparent PNGs that are overlaid over each other to build up the full picture. The problem here is that we've figured out that we'd require over 120,000 different images to cover all models, fabrics etc!!
I've looked at a few 3d texture tools such as http://www.arahne.si/products/arah-drape.html, hoping that one of them would have a CLI option where you give it a pre-created wireframe, and a fabric to overlay, and it generates the required image on the fly, but so far everything seems to require real-time use of the GUI to use it.
So, is there a CLI tool that would do what I'm after, or can anyone suggest a way to manipulate the GUI automatically? (from a tech point of view, I'm comfortable with C, Bash, Python or PHP as a solution!)
Thanks!
ArahDrape 2.2 can now work from a command line without any GUI interface. You can also call ArahDrape as a C library. In this way, it can be used in a web server to create texture mapped images on the fly. The command line options are explained below.
ArahDrape 2.2j command line version, ©2015 Arahne
usage:
adCommand -o /tmp/outputImage.png -tN /home/user/texture.png [-hidemodel] [-divide 2] [-filterPNG] [-compressPNG 2] [-m /home/user/model.png] -owner name -activation 174b3cfb49e9 /home/user/project.drape
Input and output images can have png, .tif or .jpg extensions
-o output_image_file
-tN texture_image_file [N goes from 0 to 199]
-hidemodel will render all areas not in region as white
-divide N [N goes from 2 to 5] divide resulting image pixel size
-filterPNG if you do not filter it, rendering is faster
-compressPNG N [N goes from 0 to 9] lower number saves faster, but bigger files
-m model_image_file use this if you want to replace model image from the project; must have same pixel size
-owner owner_name pass the given owner name
-activation activation_code pass the given activation code
last parameter should be ArahDrape project file
All files should be entered with full path.
If you need spaces in filenames, use quotes "" around the filename.
If you provide only Owner name, without activation code, program returns registration code.
ArahDrape supports batch export.
Open ArahDrape project, click on texture you wish to replace, put all your texture in a directory, select from menu
Textures > Browse textures, and as you click the texture to load it, program will save the draped picture. If you have thousands of images, use keyboard shortcut = and program will automatically do them all.
Alpha channel transparency is supported in loading model images or textures, and saving the draped images, as long as you use PNG or TIFF.
Please check this video to see how
ArahDrape works in batch mode.
we (http://digitaldraping.com/) can do just what you are asking. We have two options creating images and rendering a meshed image on the fly. Just get in touch if you still need this solution.
I'm having an issue with attempting to save some plots with transparent ellipsoids on them if I attempt to save them with .ps/.eps extensions.
Here's the plot saved as a .png:
If I choose to save it as a .ps/.eps here is what it looks like:
How I got around this, was to use ImageMagick to convert the original png to a ps. The only problem is that the image in png format is about 90k, and it becomes just under 4M after conversion. This is not good since I have a lot of these images, and it will take too much time to compile my latex document. Does anyone have a solution to this?
The problem is that eps does not support transparencies natively.
There are few options:
rasterize the image and embed in a eps file (like #Molly suggests) or exporting to pdf and converting with some external tool (like gs) (which usually relies as well on rasterization)
'mimic' transparency, giving a colour that looks like the transparent one on a given background.
I discussed this for sure once on the matplotlib mailing list, and I got the suggestion to rasterize, which is not feasible as you get either pixellized or huge figures. And they don't scale very nicely when put into, e.g., a publication.
I personally use the second approach, and although not ideal, I found it good enough. I wrote a small python script that implements the algorithm from this SO post to obtain a solid RGB representation of a colour with a give transparency
EDIT
In the specific case of your plot try to use the zorder keyword to order the parts plotted. Try to use zorder=10 for the blue ellipse, zorder=11 for the green and zorder=12 for the hexbins.
This way the blue should be below everything, then the green ellipse and finally the hexbins. And the plot should be readable also with solid colors. And if you like the shades of blue and green that you have in png, you can try to play with mimic_alpha.py.
EDIT 2
If you are 100% sure that you have to use eps, there are a couple of workarounds that come to my mind (and that are definitely uglier than your plot):
Just draw the ellipse borders on top of the hexbins.
Get centre and amplitude of each hexagon, (possibly discard all zero bins) and make a scatter plot using the same colour map as in hexbin and adjusting the marker size and shape as you like. You might want to redraw the ellipses borders on top of that
Another alternative would be to save them to pdf
savefig('myfigure.pdf')
That works with pdflatex, if that was the reason why you needed to use eps and not svg.
You can rasterize the figure before saving it to preserve transparency in the eps file:
ax.set_rasterized(True)
plt.savefig('rasterized_fig.eps')
I had the same problem. To avoid rasterizing, you can save the image as a pdf and then run (on unixish systems at least) in a terminal:
pdftops -eps my.pdf my.eps
Which gives a .eps file as output.
I solved this by:
1) adding a set_rasterization_zorder(1) when defining the figure area:
fxsize=16
fysize=8
f = figure(num=None, figsize=(fxsize, fysize), dpi=180, facecolor='w',
edgecolor='k')
plt.subplots_adjust(
left = (18/25.4)/fxsize,
bottom = (13/25.4)/fysize,
right = 1 - (8/25.4)/fxsize,
top = 1 - (8/25.4)/fysize)
subplots_adjust(hspace=0,wspace=0.1)
#f.suptitle('An overall title', size=20)
gs0 = gridspec.GridSpec(1, 2)
gs11 = gridspec.GridSpecFromSubplotSpec(1, 1, subplot_spec=gs0[0])
ax110 = plt.Subplot(f, gs11[0,0])
f.add_subplot(ax110)
ax110.set_rasterization_zorder(1)
2) a zorder=0 in each alpha=anynumber in the plot:
ax110.scatter(xs1,ys1 , marker='o', color='gray' , s=1.5,zorder=0,alpha=0.3)#, label=label_bg)
and
3) finally a rasterized=True when saving:
P.savefig(str(PLOTFILENAME)+'.eps', rasterized=True)
Note that this may not work as expected with the transparent keyword to savefig because an RGBA colour with alpha<1 on transparent background will be rendered the same as the RGB colour with alpha=1.
As mentioned above, the best and easiest choice (if you do not want to loose resolution) is to rasterized the figure
f = plt.figure()
f.set_rasterized(True)
ax = f.add_subplot(111)
ax.set_rasterized(True)
f.savefig('figure_name.eps',rasterized=True,dpi=300)
This way, you can manage the size by dpi option as well. In fact, you can also play with the zorder below you want to apply the rasterization:
ax.set_rasterization_zorder(0)
Note: It is important to keep f.set_rasterized(True) when you use plt.subplot and plt.subplot2grid functions. Otherwise, label and tick area will not appear in the .eps file
My solution is to export the plot as .eps, load it up to Inkscape for example, then Ungroup the plot, select the object that I want to set the transparency and just edit the Opacity of the Fill in the "Fill and Stroke" tab.
You can save the file as .svg if you want to tweak it later, or export the image for a publication.
If you are writing the academic paper in latex, I would recommend you export the .pdf file rather than .eps. The .pdf format supports transparency perfectly and has good compression efficiency, and most importantly, can be easily edited in Adobe Illustrator.
If you wanna further edit the graph (NOT EDITING DATA! I MEAN, FOR GOOD-LOOKING), you could open the exported graph, in Adobe Acrobat - Edit - Copy elements into Adobe Illustrator. The two software can handle everything perfectly.
I work happily with this method. Everything clear, editable and small-size. Hope can help.
I have a project using various members of Wikipedia's grey maps: http://en.wikipedia.org/wiki/Wikipedia:Blank_maps. I fill them in with colors depending on which countries, states or provinces a user selects by clicking on the shape or by checking a checkbox.
I would like to write a script that creates imagemaps automatically of each country, state or province by somehow getting the X and Y pixel location of the borders of a country, state or province albeit without the names of these entities, which I will fill in later. I have already done the World map by hand and found a open source US map image map demo. I would now like to create my maps more rapidly.
I use PHP and GD to floodfill the shapes, so I guess I could use one central pixel location of the shapes as well. Any suggestions? This script is a possibility but is still somewhat manual: http://abhinavsingh.com/blog/2009/03/using-image-maps-in-javascript-a-demo-application/. Also Mapedit, http://www.boutell.com/mapedit/, has a magic wand feature that works pretty well, but again I have a feeling this can be done automatically.
An almost perfect solution to this issue is by using SVG images and this translator of the svg code to imagmap area tags: http://www.electricfairground.com/polygonator/. The result is an appropriate image map, although the svg image may need to be resized, and the countries or provinces all seem to be offset and occasionally jumbled up. So this require opening a page generated with the SVG image or exported PNG copy of the SVG file, in a wysiwig editor that allows you to move imagemap elements.
I'm trying to figure out what the pattern of the offset is and if I do I'll post it here: http://wherehaveibeen.info/images/polye.html. The author of the "Polygonator" clued me into his service and using svg map images from his article here: http://www.electricfairground.com/2009/08/08/image-map-rollover-effects-using-jquerys-maphilight-plugin/. He advocates there, the tracing of png images into svg images via Inkscape. But since Wikipedia already has maps in SVG format, why not go straight to the code? It turns out that svg files basically already have the polygons separated and the border regions speciied, at least in the Wikipedia grey maps, http://en.wikipedia.org/wiki/Wikipedia:Blank_maps, they just need some cleaning up with the Polygonator.
I found if I opened up the SVG code in Notepad++ i could copy and paste in the entire contents of the SVG file and the polygonator will remove the unneeded code. A little clean up of the imagemap area tags is required afterwards but not much. The biggest problem is the mentioned generated area tags regions offests and the occasionl jumbled up overlapping locations of the imagemap areas in the generated code.
Well the real answer here appears to be that SVG files are almost imagemaps already and can be mildly processed to turn them into imagemaps, and Wikipedia certainly has plenty of SVG maps.
There are at least three projects that attempt to do this, with only some success at the moment. I'm kind of more interested in making an SVG file processing online image mapper service now that so might work on that project instead of just the map coloring one:
Polygonator - described here: http://www.electricfairground.com/2009/08/08/image-map-rollover-effects-using-jquerys-maphilight-plugin/ but the actual service is here: http://www.electricfairground.com/polygonator/index.html - is the simplest and best service or software so far I think. You have to manually dump the SVG XML text into the input field, but despite what the author says, I think you can dump the entire SVG file in the in field, not just the "M-z tag". The resulting area tags need editing to remove empty ones without coordinates and polygons with only two points.
Inkscapemap - http://sourceforge.net/projects/inkscapemap/ - chokes on complex SVG files such as those with shading. Also I couldn't get it to display as an HTML service even though I followed advice about using the main class of the jar file which I found described in the manifest file as well referring to the main jar file and the support file in an "archive" attribute.
http://davidlynch.org/blog/2008/03/creating-an-image-map-from-svg/ - very interesting project with many blog comments. The image maps again are not quite perfect and need editing.
I see I can use GD PHP's imagecolorat and cycle through all the pixels to find those that are black. This works:
<?php
$im = ImageCreateFromPNG("india.png");
$width = imagesx($im);
$height = imagesy($im);
for ($cy=0;$cy<$height;$cy++) {
echo '<p>';
for ($cx=0;$cx<$width;$cx++) {
$rgb = ImageColorAt($im, $cx, $cy);
$col = imagecolorsforindex($im, $rgb);
if ($col["red"] == 0 && $col["green"] == 0 && $col["blue"] ==0){
echo $cx.", ".$cy." ";
} else {echo "";}
}
}
?>
Can anybody suggest how to find the polygons in the huge multipolygon complex that results from running the above code on say a black and white 2 color map of India, where all the borders are black and the interior of the states and Indian Ocean is white??
Here is image of India: http://wherehaveibeen.info/images/india.png and the mess now of the coordinates for the imagemap that needs to be split up into separate polygons: http://wherehaveibeen.info/images/black.php