Dear yt-users, I am having some trouble with the yt clump finder. Mostly, my issue is that I don't understand what I am getting when I annotate the projectionplot. Instead of the nice lines in the example, I get strange filled-in circles? My figure is attached, and here is my code: ################## ds = yt.load("/mnt/ceph/users/stonnesen/runs/JO204wind/DD"+loop[i]+"/JO204cw"+loop[i]) ad = ds.all_data() data_source = ad.cut_region(["obj['z'] > 0.27"]) #ds.disk([0.5, 0.5, 0.5], [0., 0., 1.],(80, 'kpc'), (145, 'kpc')) # the field to be used for contouring field = ("gas", "density") # This is the multiplicative interval between contours. step = 2.0 # Now we set some sane min/max values between which we want to find contours # This is how we tell the clump finder what to look for -- it won't look for # contours connected below or above these threshold values. c_min = 2e-25 #10**np.floor(np.log10(data_source[field]).min()+3 ) c_max = 10**np.floor(np.log10(data_source[field]).max()+1) # Now find get our 'base' clump -- this one just covers the whole domain. master_clump = Clump(data_source, 'density') # Add a "validator" to weed out clumps with less than 16 cells. # As many validators can be added as you want. master_clump.add_validator("min_cells", 16) # Calculate center of mass for all clumps. master_clump.add_info_item("center_of_mass") # Begin clump finding. find_clumps(master_clump, c_min, c_max, step) # Save the clump tree as a reloadable dataset fn = master_clump.save_as_dataset(fields=["density"]) # Traverse the clump hierarchy to get a list of all of the 'leaf' clumps leaf_clumps = get_lowest_clumps(master_clump) # To visualize these clumps, a list of clumps can be supplied to # the "clumps" callback on a plot. First, we create a projection plot: prj = yt.ProjectionPlot(ds, 0, 'density', center=[0.5,0.5,0.5],width=(160,'kpc')) prj.set_buff_size(4000) # Next we annotate the plot with contours on the borders of the clumps prj.annotate_clumps(leaf_clumps) # Save the plot to disk. prj.save('JO204cw'+loop[i]+'_clumps_16pix') ########################## Also, when I have
print (leaf_clumps[0]["gas","density"])
I get 22 outputs, which seems like a lot less than what is getting put on the figure? Anyway, I am lost and any help would be greatly appreciated. Best, Stephanie -- Dr. Stephanie Tonnesen Associate Research Scientist CCA, Flatiron Institute New York, NY stonnes@gmail.com
