[yt-users] Creating image from FITS data

Mon Sep 11 15:03:48 PDT 2017

HI John,

Just a little update from my part. I could do the same thing with creating
a sphere of 400 arcmin and separating out the  desired value and and
drawing a circle around it with some numpy and matplotlib functions. I am
basically interested to see what function in yt can do these same things
for me. I have also attached the resulted plot.

My code looks like the following:

*from astropy.io <http://astropy.io> import fitsimport matplotlib.pyplot as
plt%matplotlib inlineimport matplotlib.image as mpimgimport numpy as
nphdulist = fits.open('signal_wfilt_sn.fits')scidata = hdulist[0].data*

*scidatah = 1629w = 1629center = [815, 815]radius = 400def
createCircularMask(h, w, center=center, radius=radius):    Y, X =
np.ogrid[:h, :w]    dist_from_center = np.sqrt((X - center[0])**2 +
(Y-center[1])**2)    mask = dist_from_center <= radius    return maskimg =
scidatah, w = img.shape[:2]mask = createCircularMask(h, w)masked_img =
img.copy()masked_img[~mask] = 0imgplot = plt.imshow(masked_img)hot =
np.where(masked_img>4.5)imgplotc=plt.colorbar()c.set_label('s/n')*

*plt.scatter(hot[0], hot[1],alpha=0.05, facecolor = "none",
edgecolor='yellow')plt.show()*

*Best*

*Tazkera *

On Sun, Sep 10, 2017 at 8:46 PM, tazkera haque <h.tazkera at gmail.com> wrote:

> Hi John,
>
> Thanks so much for all the help. I just need one more clarification from
> you. I needed to identify values greater than 4.5 and draw a circle around
> them. I used the masking function in yt to figure out the array which
> contains those certain values. But Can you please show me how do I draw
> circles around them in the same 2d plot?
>
>
>
>
>
>
>
>
> *hot = dd["image_0"].in_units('dimensionless') > 4.5print('Temperature of
> all data: dd["image_0"] = \n%s' % dd["image_0"])print("Boolean Mask: hot =
> \n%s" % hot)print('Temperature of "hot" data: dd["image_0"][hot] = \n%s'
> %      dd['image_0'][hot])q = dd['image_0'][hot]print q*
> Thanks a lot
>
> Tazkera
>
>
> On Sun, Sep 10, 2017 at 12:22 PM, John ZuHone <jzuhone at gmail.com> wrote:
>
>> Hi Tazkera,
>>
>> The issue here is that sp[“image_0”] is a 1-D array of the points in the
>> sphere. If you want to make plots using yt, I would suggest checking out
>> the plotting documentation:
>>
>> http://yt-project.org/doc/visualizing/plots.html
>>
>> Specifically, since you have a 2D fits file, it’d probably be simplest to
>> use plot_2d:
>>
>> http://yt-project.org/doc/visualizing/plots.html#plots-of-2d-datasets
>>
>> If you want to cut out the data that isn’t in your sphere object, you can
>> try passing the sphere object in as the data_source argument to plot_2d:
>>
>> p = yt.plot_2d(ds, “image_0”, data_source=sp)
>> p.save()
>>
>> That should give you a head start.
>>
>> Best,
>>
>> John
>>
>> On Sep 9, 2017, at 8:02 PM, tazkera haque <h.tazkera at gmail.com> wrote:
>>
>> Hi People,
>>
>> I am trying to play around with FITS file format. I want to create an
>> image from this file which will include data from center to 20 arc minutes.
>> each pixel is 3x3 arc sec.
>>
>> *import yt*
>> *ds = yt.load("signal_wfilt_sn.fits")*
>> *ds.print_stats()*
>>
>> *ds.field_list*
>>
>> *ds.domain_width*
>>
>> *ds.derived_field_list*
>> *dd = ds.all_data()*
>> *dd*
>>
>> *sp = ds.sphere(ds.domain_center, (400, 'code_length'))  # create sphere
>> of 20 arcminutes with 3x3 pixel size*
>>
>> *sp[("fits", "image_0")]
>>        # check array of data within the sphere*
>> *#plot 1D histogram of data over pixel*
>> *pplot = yt.ProfilePlot(sp, "image_0", ["pixel"], weight_field=None,
>> n_bins=1024, *
>> *plot_spec=dict(color='red', linestyle="--"), y_log={'pixel':False})*
>> *pplot.show()*
>> *# convert data to numpy array*
>> *import numpy as np*
>> *image = np.array(sp['image_0'])*
>>
>> *# create image?*
>> *imgplot = plt.imshow(image)*
>>
>> *imgplot*
>> *plt.show()*
>> *image*
>>
>> *The code is failing at this point with error:*
>>
>> ---------------------------------------------------------------------------TypeError                                 Traceback (most recent call last)<ipython-input-21-6a83e68fbbf2> in <module>()----> 1 imgplot = plt.imshow(image)      2       3 imgplot      4 plt.show()
>> /home/trina/anaconda2/lib/python2.7/site-packages/matplotlib/pyplot.pyc in imshow(X, cmap, norm, aspect, interpolation, alpha, vmin, vmax, origin, extent, shape, filternorm, filterrad, imlim, resample, url, hold, data, **kwargs)   3155                         filternorm=filternorm, filterrad=filterrad,   3156                         imlim=imlim, resample=resample, url=url, data=data,-> 3157                         **kwargs)   3158     finally:   3159         ax._hold = washold
>> /home/trina/anaconda2/lib/python2.7/site-packages/matplotlib/__init__.pyc in inner(ax, *args, **kwargs)   1896                     warnings.warn(msg % (label_namer, func.__name__),   1897                                   RuntimeWarning, stacklevel=2)-> 1898             return func(ax, *args, **kwargs)   1899         pre_doc = inner.__doc__   1900         if pre_doc is None:
>> /home/trina/anaconda2/lib/python2.7/site-packages/matplotlib/axes/_axes.pyc in imshow(self, X, cmap, norm, aspect, interpolation, alpha, vmin, vmax, origin, extent, shape, filternorm, filterrad, imlim, resample, url, **kwargs)   5122                               resample=resample, **kwargs)   5123 -> 5124         im.set_data(X)   5125         im.set_alpha(alpha)   5126         if im.get_clip_path() is None:
>> /home/trina/anaconda2/lib/python2.7/site-packages/matplotlib/image.pyc in set_data(self, A)    598         if (self._A.ndim not in (2, 3) or    599                 (self._A.ndim == 3 and self._A.shape[-1] not in (3, 4))):--> 600             raise TypeError("Invalid dimensions for image data")    601     602         self._imcache = None
>> TypeError: Invalid dimensions for image data
>>
>>
>> I am completely new to image processing, so I am interested to know how
>> you create image for this type of data in yt. Your help is very
>> appreciated. I also provided a link to the dataset:
>>
>> https://www.dropbox.com/s/bftuihqcoun8tny/signal_wfilt_sn.fits?dl=0
>> Thanks a lot
>> Tazkera haque
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