Mailman 3 August 2011 - yt-users

Re: [yt-users] coordinate question
by Elizabeth Tasker Aug. 23, 2011

Aug. 23, 2011

Hi Matt, Thank you, that helped, but it did not entirely solve the problem. What I've found is that a slice through my covering_grid does not look the same as a slice done using pc.add_slice. I've attached links to two images to demonstrate the issue. http://i.imgur.com/zKVzY.png shows the slice through the extracted region with the positions of the cores (found using extract_connected_sets on the whole hierarchy) which don't line up. However, if you can imagine putting those same … [View More]cores onto http://i.imgur.com/sOEvG.png which was made via add_slice, you can see they'd align perfectly. It looks like the extracted section is flipped through the line y = x. Do you know if this is a feature of imshow or of covering_grid? I'm thinking it *might* be the covering_grid that is inverted, since the results from my data analysis don't look as expected (but it was a big calculation that I could totally have just messed it up). I've put my calls for both below (and a more complete code is at the bottom of the email). extractCube = pf.h.covering_grid(extract_level, left_edge=extractLE, right_edge=extractRE, # How many dimensions along each axis dims=extractDims, # And any fields to preload (this is optional!) num_ghost_zones = 3) pylab.imshow(extractCube["NegEscapeVelocity"][:,:,int(extractDims[2]/2)], origin='lower', interpolation='nearest', aspect=aspect, extent=[min_x, max_x, min_y, max_y]) Thanks! Elizabeth Matthew Turk wrote: > Hi Elizabeth, > > The imshow command in matplotlib normally puts the origin in the upper > left. Change your call to imshow to include the argument: > > origin='lower' > > and it may fix your problem. If you look at the yt source, this is > scattered throughout to account for this. You probably also want to > supply: > > interpolation='nearest' > > -Matt > > On Mon, Aug 22, 2011 at 7:09 PM, Elizabeth Tasker > <taskere(a)mcmaster.ca> wrote: > >> Hi, >> >> I feel I have a co-ordinate problem. >> >> I have a yt script that uses extract_connected_sets to find a bunch of >> contoured objects, for which I calculate the centre of mass (core_com >> below). >> >> I then cut out a covering_grid centred on each object that is 2 kpc in >> width. >> >> I image the slice of the covering_grid through its and over-plot the >> positions of the centre of mass of the contoured objects on it. >> >> The problem is, they don't line up! >> >> cloud50.png shows the process centred on object 50. Object 50 itself is >> nicely over a blob but the others are randomly scattered. Although >> this is >> only a slice, the z-direction of the objects differs only slightly: it >> shouldn't be possible to have an object sitting over nothing (especially >> when the slice effectively shows potential, which varies smoothly). >> >> cloud51.png shows the same process now centred on object 51. 51 is >> now over >> a clear blob, but you can see that the image has moved differently to >> the >> numbers. (The image has shifted down and the numbers way up). >> >> It looks to me that this should be flipped somehow (although >> experimental >> inverting the x-y axes have failed!), but I cannot see where the >> mistake is. >> >> The (abbreviated) code looks like: >> >> contours = dd.extract_connected_sets("NegEscapeVelocity", 1, 30.0, maxv, >> log_space=False) >> allcloudcores = contours[1][0] #cores defined by contour 0 >> thiscore = allcloudcores[c] >> >> core_com = [] >> for c in range(ncores): >> core_com.append(thiscore.quantities["CenterOfMass"]()) >> >> >> extractLE = [] >> extractRE = [] >> extractDims = [] >> >> min_x, max_x = thiscore.quantities["Extrema"]("x")[0] >> min_y, max_y = thiscore.quantities["Extrema"]("y")[0] >> min_z, max_z = thiscore.quantities["Extrema"]("z")[0] >> >> extractLE.append(max(min_x-1.0, 0.0)) >> extractLE.append(max(min_y-1.0, 0.0)) >> extractLE.append(max(min_z-1.0, 0.0)) >> >> extractRE.append(min(max_x+1.0, thiscore.pf.domain_right_edge[0])) >> extractRE.append(min(max_y+1.0, thiscore.pf.domain_right_edge[1])) >> extractRE.append(min(max_z+1.0, thiscore.pf.domain_right_edge[2])) >> >> for dim in range(3): >> >> extractDims.append(round((extractRE[dim]-extractLE[dim])/cellsize)) >> >> extractCube = pf.h.covering_grid(extract_level, >> left_edge=extractLE, >> right_edge=extractRE, >> dims=extractDims, >> num_ghost_zones = 3) >> >> plotfig = pylab.figure() >> pylab.imshow(extractCube["NegEscapeVelocity"][:,:,int(extractDims[2]/2)], >> >> extent=[extractLE[0], extractRE[0], extractLE[1], extractRE[1]]) >> colorbar = pylab.colorbar() >> colorbar.set_label("Negative escape velocity [km/s]") >> pylab.xlabel('x [kpc]') >> pylab.ylabel('y [kpc]') >> >> for m in range(ncores): >> pylab.annotate('%s' % (m), xy=(core_com[m][0], core_com[m][1]), >> xycoords='data') >> >> pylab.savefig('clouds_novel%s' % (c)) >> >> >> >> >> Is this a problem of where the "zero" point is in yt / enzo / python? >> I was >> assuming (0,0,0) is the bottom left? >> >> Elizabeth >> >> _______________________________________________ >> yt-users mailing list >> yt-users(a)lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> >> > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > [View Less]

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line callback
by Luigi Iapichino Aug. 23, 2011

Aug. 23, 2011

Dear all, I would like to overplot a line to a slice of mine. I use the line callback, for example with the following sintax: p.modify["line"]((0,639),(30,30)) if I have well understood, the two pairs of numbers are pixel-based coordinates. I have a few questions: 1) where is the range of these number set (i.e., the image size in pixel), and how can I eventually modify it? 2) Is it any simple way to define the begin and end points of a line in other coordinates? Code coordinates from 0 … [View More]

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coordinate question
by Elizabeth Tasker Aug. 23, 2011

Aug. 23, 2011

Hi, I feel I have a co-ordinate problem. I have a yt script that uses extract_connected_sets to find a bunch of contoured objects, for which I calculate the centre of mass (core_com below). I then cut out a covering_grid centred on each object that is 2 kpc in width. I image the slice of the covering_grid through its and over-plot the positions of the centre of mass of the contoured objects on it. The problem is, they don't line up! cloud50.png shows the process centred on object 50. … [View More]Object 50 itself is nicely over a blob but the others are randomly scattered. Although this is only a slice, the z-direction of the objects differs only slightly: it shouldn't be possible to have an object sitting over nothing (especially when the slice effectively shows potential, which varies smoothly). cloud51.png shows the same process now centred on object 51. 51 is now over a clear blob, but you can see that the image has moved differently to the numbers. (The image has shifted down and the numbers way up). It looks to me that this should be flipped somehow (although experimental inverting the x-y axes have failed!), but I cannot see where the mistake is. The (abbreviated) code looks like: contours = dd.extract_connected_sets("NegEscapeVelocity", 1, 30.0, maxv, log_space=False) allcloudcores = contours[1][0] #cores defined by contour 0 thiscore = allcloudcores[c] core_com = [] for c in range(ncores): core_com.append(thiscore.quantities["CenterOfMass"]()) extractLE = [] extractRE = [] extractDims = [] min_x, max_x = thiscore.quantities["Extrema"]("x")[0] min_y, max_y = thiscore.quantities["Extrema"]("y")[0] min_z, max_z = thiscore.quantities["Extrema"]("z")[0] extractLE.append(max(min_x-1.0, 0.0)) extractLE.append(max(min_y-1.0, 0.0)) extractLE.append(max(min_z-1.0, 0.0)) extractRE.append(min(max_x+1.0, thiscore.pf.domain_right_edge[0])) extractRE.append(min(max_y+1.0, thiscore.pf.domain_right_edge[1])) extractRE.append(min(max_z+1.0, thiscore.pf.domain_right_edge[2])) for dim in range(3): extractDims.append(round((extractRE[dim]-extractLE[dim])/cellsize)) extractCube = pf.h.covering_grid(extract_level, left_edge=extractLE, right_edge=extractRE, dims=extractDims, num_ghost_zones = 3) plotfig = pylab.figure() pylab.imshow(extractCube["NegEscapeVelocity"][:,:,int(extractDims[2]/2)], extent=[extractLE[0], extractRE[0], extractLE[1], extractRE[1]]) colorbar = pylab.colorbar() colorbar.set_label("Negative escape velocity [km/s]") pylab.xlabel('x [kpc]') pylab.ylabel('y [kpc]') for m in range(ncores): pylab.annotate('%s' % (m), xy=(core_com[m][0], core_com[m][1]), xycoords='data') pylab.savefig('clouds_novel%s' % (c)) Is this a problem of where the "zero" point is in yt / enzo / python? I was assuming (0,0,0) is the bottom left? Elizabeth [View Less]

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creating sunrise files from RAMSES snapshot
by Robert Feldmann Aug. 22, 2011

Aug. 22, 2011

Hi, I am trying to create SUNRISE files for a RAMSES snapshot. I am using the latest stable version of YT ("2.1stable"). I can read the RAMSES snapshot, but the sunrise_exporter routine fails. The reason, it seems, is that it wants to access a field "InitialTime" that actually does not exist (see below). Is there somewhere some additional information about how to convert RAMSES to SUNRISE using YT? I could not find much (that includes searching the mailing lists). Thanks Robert >>… [View More]> pf = load("output_00105/info_00105.txt") output_00105/amr_00105.out00001 yt : [INFO ] 2011-08-21 00:09:47,343 Parameters: current_time = -1.23236270587e+17 yt : [INFO ] 2011-08-21 00:09:47,343 Parameters: domain_dimensions = [2 2 2] yt : [INFO ] 2011-08-21 00:09:47,344 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2011-08-21 00:09:47,344 Parameters: domain_right_edge = [ 1. 1. 1.] yt : [INFO ] 2011-08-21 00:09:47,344 Parameters: cosmological_simulation = 1 yt : [INFO ] 2011-08-21 00:09:47,345 Parameters: current_redshift = 1.00027409463 yt : [INFO ] 2011-08-21 00:09:47,345 Parameters: omega_lambda = 0.759999990463 yt : [INFO ] 2011-08-21 00:09:47,345 Parameters: omega_matter = 0.239999994636 yt : [INFO ] 2011-08-21 00:09:47,345 Parameters: hubble_constant = 73.0 Now, when I try the following I get an error >>> from yt.analysis_modules.sunrise_export import sunrise_exporter >>> sunrise_exporter.export_to_sunrise(pf,"analysis/yt/HYDRO_L2_18_GF_epsstar0d1") yt : [INFO ] 2011-08-21 00:11:30,744 Re-gridding level 0: 1 octree grids Re-gridding 100% ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:00 ... Re-gridding 100% ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:0 yt : [INFO ] 2011-08-21 00:11:46,711 Final grid count: 302 yt : [INFO ] 2011-08-21 00:11:46,775 Re-gridding level 16: 59069 octree grids Re-gridding 100% ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:0 yt : [INFO ] 2011-08-21 00:11:47,093 Final grid count: 153 yt : [INFO ] 2011-08-21 00:11:52,568 Getting field particle_type from 2894 yt : [INFO ] 2011-08-21 00:11:52,760 Getting field particle_position_x from 2894 yt : [INFO ] 2011-08-21 00:11:52,951 Getting field particle_position_y from 2894 yt : [INFO ] 2011-08-21 00:11:53,141 Getting field particle_position_z from 2894 yt : [INFO ] 2011-08-21 00:11:53,344 Getting field particle_velocity_x from 2894 yt : [INFO ] 2011-08-21 00:11:53,542 Getting field particle_velocity_y from 2894 yt : [INFO ] 2011-08-21 00:11:53,739 Getting field particle_velocity_z from 2894 --------------------------------------------------------------------------- KeyError Traceback (most recent call last) /d/scratch39/feldmann/local/yt/yt-x86_64/src/yt-hg/scripts/iyt in <module>() ----> 1 2 3 4 5 /d/scratch39/feldmann/local/yt/yt-x86_64/src/yt-hg/yt/analysis_modules/sunrise_export/sunrise_exporter.pyc in export_to_sunrise(pf, fn, write_particles, sub gion_bounds, particle_mass, particle_pos, particle_age, particle_metal) 110 # Velocity is cm/s, we want it to be kpc/yr 111 vel *= (pf["kpc"]/pf["cm"]) / (365*24*3400.) --> 112 age = pf["years"] * (pf["InitialTime"] - reg["creation_time"][pi]) 113 creation_time = reg["creation_time"][pi] * pf["years"] 114 /d/scratch39/feldmann/local/yt/yt-x86_64/src/yt-hg/yt/data_objects/static_output.pyc in __getitem__(self, key) 117 self.conversion_factors]: 118 if key in d: return d[key] --> 119 raise KeyError(key) 120 121 def keys(self): KeyError: 'InitialTime' --- These are the available fields in pf pf._StaticOutput__hierarchy pf.__repr__ pf._setup_nounits_units pf.has_key pf.__class__ pf.__setattr__ pf.basename pf.hierarchy pf.__delattr__ pf.__sizeof__ pf.conversion_factors pf.hubble_constant pf.__dict__ pf.__str__ pf.cosmological_simulation pf.keys pf.__doc__ pf.__subclasshook__ pf.current_redshift pf.omega_lambda pf.__format__ pf.__weakref__ pf.current_time pf.omega_matter pf.__getattribute__ pf._fieldinfo_class pf.data_style pf.parameter_filename pf.__getitem__ pf._get_hierarchy pf.dimensionality pf.parameters pf.__hash__ pf._handle pf.directory pf.print_key_parameters pf.__init__ pf._hash pf.domain_dimensions pf.ramses_tree pf.__iter__ pf._hierarchy_class pf.domain_left_edge pf.refine_by pf.__metaclass__ pf._instantiated pf.domain_right_edge pf.storage_filename pf.__module__ pf._is_valid pf.field_info pf.time_units pf.__new__ pf._parse_parameter_file pf.fullpath pf.unique_identifier pf.__reduce__ pf._set_hierarchy pf.get_smallest_appropriate_unit pf.units pf.__reduce_ex__ pf._set_units pf.h [View Less]

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shape mismatch?
by david collins Aug. 20, 2011

Aug. 20, 2011

Hi, all-- I have this simulation that has a single subgrid. 64^3 root, 24 zone root grid (from 0.15625 to 0.34375 along each axis) With the old output style (enzo1.0.1) this doesn't give me any problems. But with the new output version (packed IO, newgridio-no, in mhdctmerge) I get the following message3 <trace> >>> pf = MyOutputs.FileStaticOutputFourPi('/Users/dccollins/ThisScratch/param//Turbulence/t64_1lev_m/./DD0001/data0001') >>> pf.h Traceback (most recent … [View More]

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The yt Project
by Matthew Turk Aug. 20, 2011

Aug. 20, 2011

Hi all, In keeping with the current direction of the yt project, on the yt-dev mailing list there was some discussion recently about the mission statement of the project, the scope, and the directions we want to take it in the future. These goals have grown with time and the scope of the project has expanded, as the mission statement on the front page indicates. In keeping with this, Britton Smith proposed on yt-dev yesterday that we migrate from the ".enzotools.org" domain toward something … [View More]

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problem accessing EOSCriticalDensity parameter (enzo)
by j s oishi Aug. 18, 2011

Aug. 18, 2011

Hi all, I am trying to reach Enzo's EOSCriticalDensity parameter in my pf within yt (hg hash 486d7131f1c2) . For some reason, it throws a KeyError, even though grepping EOSCriticalDensity in the DD0001/data0001 file turns it right up: $ grep EOSCriticalDensity DD0001/data0001 EOSCriticalDensity = 1e-13 I have deleted the .yt file, but to no avail. The error message is: In [1]: pf['EOSCriticalDensity'] --------------------------------------------------------------------------- … [View More]

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Re: [yt-users] Images of extracted regions
by Elizabeth Tasker Aug. 18, 2011

Aug. 18, 2011

I've just seen that "data_source" is an option for add_projection, but it still fails with "AttributeError: 'AMRCoveringGrid' object has no attribute '_get_cut_mask'" Elizabeth Elizabeth Tasker wrote: > Hi Britton, > > Sorry, could you give me an example of how the call should look? > > I tried: > > p = pc.add_slice("NegEscapeVelocity", 2, field_parameters = > {'disk_radius':profile["DiskRadius"], > 'potential':profile["PotentialField"]}, data_source=… [View More]extractCube) > > which fails because data_source is unrecognised (and indeed, isn't in > the function description: > http://yt.enzotools.org/doc/reference/api/generated/yt.visualization.plot_c…) > > > And I tried: > > p = pc.add_slice(extractCube, "NegEscapeVelocity", 2) > > > which also failed with: > > > ValueError Traceback (most recent call > last) > > /1/home/taskere/yt/scripts/iyt in <module>() > ----> 1 > 2 > 3 > 4 > 5 > /1/home/taskere/yt/yt/visualization/plot_collection.py in > add_slice(self, field, axis, coord, center, use_colorbar, figure, > axes, fig_size, periodic, obj, > field_parameters) > 402 if field_parameters == None: field_parameters = > {} 403 obj = > self.pf.hierarchy.slice(axis, coord, > field, --> > 404 center=center, > **field_parameters) > 405 p = > self._add_plot(SlicePlot( > > 406 obj, field, > use_colorbar=use_colorbar, > /1/home/taskere/yt/yt/data_objects/data_containers.py in > __init__(self, axis, coord, fields, center, pf, node_name, **kwargs) > 935 self.coord = coord > 936 if node_name is False: > --> 937 self._refresh_data() > 938 else: > 939 if node_name is True: self._deserialize() > > /1/home/taskere/yt/yt/data_objects/data_containers.py in > _refresh_data(self) > 273 """ > 274 self.clear_data() > --> 275 self.get_data() > 276 > 277 def keys(self): > > /1/home/taskere/yt/yt/data_objects/data_containers.py in > get_data(self, fields) > 780 # We take a 3-tuple of the coordinate we want to slice > through, as well > > 781 # as the axis we're slicing along > > --> 782 self._get_list_of_grids() > 783 if not self.has_key('pdx'): > 784 self._generate_coords() > > /1/home/taskere/yt/yt/data_objects/data_containers.py in > _get_list_of_grids(self) > 994 > 995 def _get_list_of_grids(self): > --> 996 goodI = ((self.pf.h.grid_right_edge[:,self.axis] > > self.coord) > 997 & (self.pf.h.grid_left_edge[:,self.axis] <= > self.coord )) > 998 self._grids = self.pf.h.grids[goodI] # Using sources > not hierarchy > > ValueError: setting an array element with a sequence. > > > > Elizabeth > > > > > > Britton Smith wrote: >> The first is definitely possible. Just add data_source=extractCube >> to your call to add_projection or add_slice or whatever. The second >> probably won't work because the projection or slice routine will look >> for other things like cell dxs that won't be present from just a >> similarly sized array. If you want to do something like that, you're >> probably better off making a new field and then projecting that with >> the above data_source keyword argument in there. >> >> Britton >> >> On Thu, Aug 18, 2011 at 10:59 AM, Elizabeth Tasker >> <taskere(a)mcmaster.ca <mailto:taskere@mcmaster.ca>> wrote: >> >> Hi, >> >> Is it possible to make a slice or projection of a extracted, fixed >> resolution region? i.e. the resultant object of: >> >> extractCube = pf.h.covering_grid(extract_level, >> left_edge=extractLE, >> right_edge=extractRE, >> # How many dimensions along >> each axis >> dims=extractDims, >> # And any fields to preload >> (this is optional!) >> fields=["PotentialField"], >> num_ghost_zones = 3) >> >> >> Or of an array later made to the same size? e.g. >> >> cloud = na.zeros(extractCube["x-velocity"].shape, dtype='float64') >> >> >> Elizabeth >> _______________________________________________ >> yt-users mailing list >> yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> yt-users mailing list >> yt-users(a)lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org [View Less]

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Images of extracted regions
by Elizabeth Tasker Aug. 18, 2011

Aug. 18, 2011

Hi, Is it possible to make a slice or projection of a extracted, fixed resolution region? i.e. the resultant object of: extractCube = pf.h.covering_grid(extract_level, left_edge=extractLE, right_edge=extractRE, # How many dimensions along each axis dims=extractDims, # And any fields to … [View More]

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data.LeftEdge with slice?
by Elizabeth Tasker Aug. 18, 2011

Aug. 18, 2011

Hi, I have a field which uses data.LeftEdge, but when I try to create a slice from this, it says: AttributeError: 'AMRSlice' object has no attribute 'LeftEdge' Is this because the data is not 3d? I was trying valiantly to avoid having to load all that in! Elizabeth

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