[yt-users] Problem dealing with FITS data in yt
Nathan Goldbaum
nathan12343 at gmail.com
Fri Sep 8 12:28:59 PDT 2017
The fix is only available if you build yt from the git repository for now.
We will do a release sometime in the next few weeks to make the fix
generally available.
For now, you can install yt from git following these steps:
$ conda uninstall yt
$ git clone https://github.com/yt-project/yt
$ cd yt
$ pip install -e .
-Nathan
On Fri, Sep 8, 2017 at 2:21 PM, tazkera haque <h.tazkera at gmail.com> wrote:
> 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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