[yt-users] Problem dealing with FITS data in yt

tazkera haque h.tazkera at gmail.com
Fri Sep 8 12:21:07 PDT 2017


Hi Nathan,

Thanks. I see the bug has been fixed according to the post, but I am still
getting the same error with that file. I updated yt to the latest version
and rebooted my laptop. Do I need to do anything else to get it work out?

Best
Tazkera

On Thu, Sep 7, 2017 at 3:37 PM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:

> I've opened an issue, let's move discussion over there:
>
> https://github.com/yt-project/yt/issues/1552
>
> Tazkera, you can subscribe to notifications on the issue by clicking the
> subscribe button.
>
> On Thu, Sep 7, 2017 at 2:35 PM, John Zuhone <jzuhone at gmail.com> wrote:
>
>> Hi Tazkera,
>>
>> Thanks for uploading your file—it will make it far simpler to debug. I’ll
>> have a look at this and get back to you.
>>
>> Best,
>>
>> John
>>
>> On Sep 7, 2017, at 3:24 PM, tazkera haque <h.tazkera at gmail.com> wrote:
>>
>> HI People,
>>
>> I am sorry to ask you a very novice question, but I am new to deal with
>> FITS data and I wanted to load it into yt to do some processing. I uploaded
>> my file here.
>>
>> First of all, I am trying to load my first FITS data in yt and it returns
>> me an error which I don't understand:
>>
>> *import yt*
>>
>>
>>
>> *ds = yt.load("signal_wfilt_sn.fits")ds.print_stats()*
>>
>>
>> *the error:*
>>
>> yt : [WARNING  ] 2017-09-07 15:12:42,963 Cannot find time
>> yt : [INFO     ] 2017-09-07 15:12:42,965 Detected these axes: RA---TAN DEC--TAN
>> yt : [WARNING  ] 2017-09-07 15:12:42,979 No length conversion provided. Assuming 1 = 1 cm.
>> yt : [INFO     ] 2017-09-07 15:12:42,996 Parameters: current_time              = 0.0
>> yt : [INFO     ] 2017-09-07 15:12:42,997 Parameters: domain_dimensions         = [1629 1629    1]
>> yt : [INFO     ] 2017-09-07 15:12:43,001 Parameters: domain_left_edge          = [ 0.5  0.5  0.5]
>> yt : [INFO     ] 2017-09-07 15:12:43,004 Parameters: domain_right_edge         = [  1.62950000e+03   1.62950000e+03   1.50000000e+00]
>> yt : [INFO     ] 2017-09-07 15:12:43,006 Parameters: cosmological_simulation   = 0.0
>>
>> ---------------------------------------------------------------------------IndexError                                Traceback (most recent call last)<ipython-input-38-71d5999c6b09> in <module>()      1 import yt      2 ds2 = yt.load("/home/trina/Documents/ASTRO_732/A-01/signal_wfilt_sn.fits")----> 3 ds2.print_stats()
>> /home/trina/anaconda2/lib/python2.7/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.pyc in root_only(*args, **kwargs)    318     def root_only(*args, **kwargs):    319         if not parallel_capable:--> 320             return func(*args, **kwargs)    321         comm = _get_comm(args)    322         rv = None
>> /home/trina/anaconda2/lib/python2.7/site-packages/yt/data_objects/static_output.pyc in print_stats(self)    455     @parallel_root_only    456     def print_stats(self):--> 457         self.index.print_stats()    458     459     @property
>> /home/trina/anaconda2/lib/python2.7/site-packages/yt/data_objects/static_output.pyc in index(self)    417                 raise RuntimeError("You should not instantiate Dataset.")    418             self._instantiated_index = self._index_class(--> 419                 self, dataset_type=self.dataset_type)    420             # Now we do things that we need an instantiated index for    421             # ...first off, we create our field_info now.
>> /home/trina/anaconda2/lib/python2.7/site-packages/yt/frontends/fits/data_structures.pyc in __init__(self, ds, dataset_type)     90         self._handle = ds._handle     91         self.float_type = np.float64---> 92         GridIndex.__init__(self,ds,dataset_type)     93      94     def _initialize_data_storage(self):
>> /home/trina/anaconda2/lib/python2.7/site-packages/yt/geometry/geometry_handler.pyc in __init__(self, ds, dataset_type)     56         # potentially quite expensive, and should be done with the indexing.     57         mylog.debug("Detecting fields.")---> 58         self._detect_output_fields()     59      60     def _initialize_state_variables(self):
>> /home/trina/anaconda2/lib/python2.7/site-packages/yt/frontends/fits/data_structures.pyc in _detect_output_fields(self)    171                     continue    172                 if self._ensure_same_dims(hdu):--> 173                     units = self._determine_image_units(hdu.header, known_units)    174                     try:    175                         # Grab field name from btype
>> /home/trina/anaconda2/lib/python2.7/site-packages/yt/frontends/fits/data_structures.pyc in _determine_image_units(self, header, known_units)    116                     n += 1    117             if n != len(units): field_units = "dimensionless"--> 118             if field_units[0] == "/":    119                 field_units = "1%s" % field_units    120             return field_units
>> IndexError: string index out of range
>>
>> Can you Please suggest me how to load and work on this data?
>>
>> My goal is to create an image from the signal to noise data in the data file 'signal_wfilt_sn.fits' using only data
>> within 20 arcminutes of the center of the image. the pixel size is 3x3 arc second
>>
>> I had an initial code in mind which will create a sphere with a radius of 20 arcminute:
>>
>>
>>
>>
>>
>>
>> *import ytds = yt.load("signal_wfilt_sn.fits")ds.print_stats()sp = ds.sphere(ds.domain_center, (400, 'code_length'))*
>>
>> However, I first need to be able to load and explore the data. Your help and suggestion is greatly appreciated.
>>
>> Thanks a lot
>>
>>
>> Tazkera
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> ​​
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