[yt-users] Problem dealing with FITS data in yt
tazkera haque
h.tazkera at gmail.com
Fri Sep 8 16:14:04 PDT 2017
Thanks much for all the help
On Fri, Sep 8, 2017 at 5:15 PM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:
> You shouldn't be doing "sudo pip install", that means you're invoking the
> pip associated with the root account, not the pip associated with your
> anaconda installation. Try doing "conda update cython". Also make sure you
> have pip installed in your conda environment, "conda install pip".
>
> On Fri, Sep 8, 2017 at 4:10 PM, tazkera haque <h.tazkera at gmail.com> wrote:
>
>> Hi Nathan ,
>>
>> I encountered an error after
>>
>> $pip install -e .
>>
>> RuntimeError: Building yt from source requires Cython 0.24 or newer but
>> Cython 0.23.4 is installed. Please update Cython using the appropriate
>>
>> so i did
>> $ cdh
>> $ sudo pip install --upgrade Cython
>> $ Requirement already up-to-date: Cython in /usr/local/lib/python2.7/dist-
>> packages
>> Cleaning up...
>> $ cython --version
>> $ Cython version 0.23.4
>>
>> so how do I upgrade to cython 0.24? DO I need to do that inside the yt
>> directory?
>>
>> On Fri, Sep 8, 2017 at 3:36 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>> wrote:
>>
>>> Then you already have a directory named "yt". Delete it and make the
>>> clone, or clone to a new directory:
>>>
>>> $ git clone https://github.com/yt-project/yt ./yt-repo
>>>
>>> On Fri, Sep 8, 2017 at 2:35 PM, tazkera haque <h.tazkera at gmail.com>
>>> wrote:
>>>
>>>> OK Thanks. I $conda uninstall yt and then
>>>>
>>>> $ git clone https://github.com/yt-project/yt
>>>> fatal: destination path 'yt' already exists and is not an empty
>>>> directory.
>>>>
>>>>
>>>>
>>>>
>>>> On Fri, Sep 8, 2017 at 3:28 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>>>> wrote:
>>>>
>>>>> 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
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> <signal_wfilt_sn.fits>______________________________________
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>>>>>>>>
>>>>>>>>
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