Hello John I am using spyder to run the script. Spyder is using the 1.8.2 version. CheersAlex From: jzuhone@gmail.com Date: Tue, 25 Aug 2015 09:54:31 -0400 To: yt-users@lists.spacepope.org Subject: Re: [yt-users] problem with units Hi Alex, Sorry for the trouble--I'll see if I can figure out what's gone wrong on this end. It looks like you're running yt 3.2--can you tell me what version of NumPy you are running? Best, John John ZuHone Kavli Center for Astrophysics and Space Research Massachusetts Institute of Technology 77 Massachusetts Ave., 37-582G Cambridge, MA 02139 (w) 617-253-2354 (m) 781-708-5004 jzuhone@space.mit.edu jzuhone@gmail.com http://www.jzuhone.com On Aug 25, 2015, at 9:41 AM, alex volioths <alex-volos@hotmail.com> wrote: Hello everyone, I've been practicing with the example "Creating a X-ray observation from an in-memory dataset" from here http://yt-project.org/doc/analyzing/analysis_modules/photon_simulator.html However even with simple copy and paste after defining the photons I get this error message: File "/usr/local/lib/python2.7/dist-packages/spyderlib/widgets/externalshell/sitecustomize.py", line 685, in runfile execfile(filename, namespace) File "/usr/local/lib/python2.7/dist-packages/spyderlib/widgets/externalshell/sitecustomize.py", line 78, in execfile builtins.execfile(filename, *where) File "/home/afi/Documents/X_ray_sim/X_mock.py", line 75, in <module> exp_time, thermal_model, center="c") File "/usr/local/lib/python2.7/dist-packages/yt-3.2-py2.7-linux-x86_64.egg/yt/analysis_modules/photon_simulator/photon_simulator.py", line 330, in from_scratch photons = photon_model(data_source, parameters) File "/usr/local/lib/python2.7/dist-packages/yt-3.2-py2.7-linux-x86_64.egg/yt/analysis_modules/photon_simulator/photon_models.py", line 140, in __call__ kT_bins = np.linspace(kT_min, max(my_kT_max, kT_max), num=n_kT+1) File "/usr/lib/python2.7/dist-packages/numpy/core/function_base.py", line 87, in linspace step = (stop-start)/float((num-1)) File "/usr/local/lib/python2.7/dist-packages/yt-3.2-py2.7-linux-x86_64.egg/yt/units/yt_array.py", line 745, in __sub__ ro = sanitize_units_add(self, right_object, "subtraction") File "/usr/local/lib/python2.7/dist-packages/yt-3.2-py2.7-linux-x86_64.egg/yt/units/yt_array.py", line 134, in sanitize_units_add raise YTUnitOperationError(op_string, inp.units, dimensionless) YTUnitOperationError: The subtraction operator for YTArrays with units (keV) and (1) is not well defined. Any ideas? I am new to yt and i can't see something wrong. Thnak you Alex Creating a X-ray observation from an in-memory datasetCreating a X-ray observation from an in-memory dataset _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

Hi John, I am sorry for the late reply. I use spyder which comes with modules installed. Thank you for your help! Alex From: jzuhone@gmail.com Date: Wed, 26 Aug 2015 17:50:44 -0400 To: yt-users@lists.spacepope.org Subject: Re: [yt-users] problem with units Alex, My apologies—this is a bug in the code. I have a fix, which I hope to have ready by tonight or tomorrow. Just a quick question—how did you install yt? It looks like your Python stack is in /usr/local. Best, John On Aug 26, 2015, at 3:26 AM, alex volioths <alex-volos@hotmail.com> wrote:Hello John I am using spyder to run the script. Spyder is using the 1.8.2 version. CheersAlex From: jzuhone@gmail.com Date: Tue, 25 Aug 2015 09:54:31 -0400 To: yt-users@lists.spacepope.org Subject: Re: [yt-users] problem with units Hi Alex, Sorry for the trouble--I'll see if I can figure out what's gone wrong on this end. It looks like you're running yt 3.2--can you tell me what version of NumPy you are running? Best, John John ZuHone Kavli Center for Astrophysics and Space Research Massachusetts Institute of Technology 77 Massachusetts Ave., 37-582G Cambridge, MA 02139 (w) 617-253-2354 (m) 781-708-5004 jzuhone@space.mit.edu jzuhone@gmail.com http://www.jzuhone.com On Aug 25, 2015, at 9:41 AM, alex volioths <alex-volos@hotmail.com> wrote: Hello everyone, I've been practicing with the example "Creating a X-ray observation from an in-memory dataset" from here http://yt-project.org/doc/analyzing/analysis_modules/photon_simulator.html However even with simple copy and paste after defining the photons I get this error message: File "/usr/local/lib/python2.7/dist-packages/spyderlib/widgets/externalshell/sitecustomize.py", line 685, in runfile execfile(filename, namespace) File "/usr/local/lib/python2.7/dist-packages/spyderlib/widgets/externalshell/sitecustomize.py", line 78, in execfile builtins.execfile(filename, *where) File "/home/afi/Documents/X_ray_sim/X_mock.py", line 75, in <module> exp_time, thermal_model, center="c") File "/usr/local/lib/python2.7/dist-packages/yt-3.2-py2.7-linux-x86_64.egg/yt/analysis_modules/photon_simulator/photon_simulator.py", line 330, in from_scratch photons = photon_model(data_source, parameters) File "/usr/local/lib/python2.7/dist-packages/yt-3.2-py2.7-linux-x86_64.egg/yt/analysis_modules/photon_simulator/photon_models.py", line 140, in __call__ kT_bins = np.linspace(kT_min, max(my_kT_max, kT_max), num=n_kT+1) File "/usr/lib/python2.7/dist-packages/numpy/core/function_base.py", line 87, in linspace step = (stop-start)/float((num-1)) File "/usr/local/lib/python2.7/dist-packages/yt-3.2-py2.7-linux-x86_64.egg/yt/units/yt_array.py", line 745, in __sub__ ro = sanitize_units_add(self, right_object, "subtraction") File "/usr/local/lib/python2.7/dist-packages/yt-3.2-py2.7-linux-x86_64.egg/yt/units/yt_array.py", line 134, in sanitize_units_add raise YTUnitOperationError(op_string, inp.units, dimensionless) YTUnitOperationError: The subtraction operator for YTArrays with units (keV) and (1) is not well defined. Any ideas? I am new to yt and i can't see something wrong. Thnak you Alex _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org______________... mailing listyt-users@lists.spacepope.orghttp://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

Hi John, thank you for your time and help. I used conda to install yt. I am using Ubuntu 14 LTS but I am a newbie. Again, thank you. Alex From: jzuhone@gmail.com Date: Mon, 31 Aug 2015 17:49:51 -0400 To: yt-users@lists.spacepope.org Subject: Re: [yt-users] problem with units Hi Alex, Sorry—the delays on my end are longer than yours. We’ve fixed this bug, but I’m still a little unclear as to how you installed yt. You’re using spyder to run the script, but I don’t think you can install yt using spyder, so you must have used “pip install yt” to install it, or maybe you installed it from source. Do you remember how you did it? Also, is this Linux or Mac OS X? Best, John On Aug 29, 2015, at 1:28 PM, alex volioths <alex-volos@hotmail.com> wrote:Hi John, I am sorry for the late reply. I use spyder which comes with modules installed. Thank you for your help! Alex From: jzuhone@gmail.com Date: Wed, 26 Aug 2015 17:50:44 -0400 To: yt-users@lists.spacepope.org Subject: Re: [yt-users] problem with units Alex, My apologies—this is a bug in the code. I have a fix, which I hope to have ready by tonight or tomorrow. Just a quick question—how did you install yt? It looks like your Python stack is in /usr/local. Best, John On Aug 26, 2015, at 3:26 AM, alex volioths <alex-volos@hotmail.com> wrote:Hello John I am using spyder to run the script. Spyder is using the 1.8.2 version. CheersAlex From: jzuhone@gmail.com Date: Tue, 25 Aug 2015 09:54:31 -0400 To: yt-users@lists.spacepope.org Subject: Re: [yt-users] problem with units Hi Alex, Sorry for the trouble--I'll see if I can figure out what's gone wrong on this end. It looks like you're running yt 3.2--can you tell me what version of NumPy you are running? Best, John John ZuHone Kavli Center for Astrophysics and Space Research Massachusetts Institute of Technology 77 Massachusetts Ave., 37-582G Cambridge, MA 02139 (w) 617-253-2354 (m) 781-708-5004 jzuhone@space.mit.edu jzuhone@gmail.com http://www.jzuhone.com On Aug 25, 2015, at 9:41 AM, alex volioths <alex-volos@hotmail.com> wrote: Hello everyone, I've been practicing with the example "Creating a X-ray observation from an in-memory dataset" from here http://yt-project.org/doc/analyzing/analysis_modules/photon_simulator.html However even with simple copy and paste after defining the photons I get this error message: File "/usr/local/lib/python2.7/dist-packages/spyderlib/widgets/externalshell/sitecustomize.py", line 685, in runfile execfile(filename, namespace) File "/usr/local/lib/python2.7/dist-packages/spyderlib/widgets/externalshell/sitecustomize.py", line 78, in execfile builtins.execfile(filename, *where) File "/home/afi/Documents/X_ray_sim/X_mock.py", line 75, in <module> exp_time, thermal_model, center="c") File "/usr/local/lib/python2.7/dist-packages/yt-3.2-py2.7-linux-x86_64.egg/yt/analysis_modules/photon_simulator/photon_simulator.py", line 330, in from_scratch photons = photon_model(data_source, parameters) File "/usr/local/lib/python2.7/dist-packages/yt-3.2-py2.7-linux-x86_64.egg/yt/analysis_modules/photon_simulator/photon_models.py", line 140, in __call__ kT_bins = np.linspace(kT_min, max(my_kT_max, kT_max), num=n_kT+1) File "/usr/lib/python2.7/dist-packages/numpy/core/function_base.py", line 87, in linspace step = (stop-start)/float((num-1)) File "/usr/local/lib/python2.7/dist-packages/yt-3.2-py2.7-linux-x86_64.egg/yt/units/yt_array.py", line 745, in __sub__ ro = sanitize_units_add(self, right_object, "subtraction") File "/usr/local/lib/python2.7/dist-packages/yt-3.2-py2.7-linux-x86_64.egg/yt/units/yt_array.py", line 134, in sanitize_units_add raise YTUnitOperationError(op_string, inp.units, dimensionless) YTUnitOperationError: The subtraction operator for YTArrays with units (keV) and (1) is not well defined. Any ideas? I am new to yt and i can't see something wrong. Thnak you Alex _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org______________... mailing listyt-users@lists.spacepope.orghttp://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org______________... mailing listyt-users@lists.spacepope.orghttp://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

Hello John, I decided to upgrade now to give some feedback that could be useful. After the update command I get: Fetching package metadata: ......Solving package specifications: .# All requested packages already installed.# packages in environment at /home/afi/miniconda:#yt 3.2 np19py27_0 when I run the script from the terminal and not from spyder I get this warning: YTUnitOperationError Traceback (most recent call last)/home/afi/Documents/X_ray_sim/X_mock.py in <module>() 73 74 photons = PhotonList.from_scratch(sphere, redshift, A,---> 75 exp_time, thermal_model, center="c") 76 77 /home/afi/miniconda/lib/python2.7/site-packages/yt/analysis_modules/photon_simulator/photon_simulator.pyc in from_scratch(cls, data_source, redshift, area, exp_time, photon_model, parameters, center, dist, cosmology) 328 parameters["Width"] = 2.*width.in_units("kpc") 329 --> 330 photons = photon_model(data_source, parameters) 331 332 mylog.info("Finished generating photons.") /home/afi/miniconda/lib/python2.7/site-packages/yt/analysis_modules/photon_simulator/photon_models.pyc in __call__(self, data_source, parameters) 138 idxs = np.argsort(kT) 139 --> 140 kT_bins = np.linspace(kT_min, max(my_kT_max, kT_max), num=n_kT+1) 141 dkT = kT_bins[1]-kT_bins[0] 142 kT_idxs = np.digitize(kT[idxs], kT_bins) /home/afi/miniconda/lib/python2.7/site-packages/numpy/core/function_base.pyc in linspace(start, stop, num, endpoint, retstep, dtype) 96 if num == 1: 97 return array([start], dtype=dtype)---> 98 step = (stop-start)/float((num-1)) 99 y = _nx.arange(0, num, dtype=dtype) * step + start 100 y[-1] = stop /home/afi/miniconda/lib/python2.7/site-packages/yt/units/yt_array.pyc in __sub__(self, right_object) 743 744 """--> 745 ro = sanitize_units_add(self, right_object, "subtraction") 746 return YTArray(super(YTArray, self).__sub__(ro)) 747 /home/afi/miniconda/lib/python2.7/site-packages/yt/units/yt_array.pyc in sanitize_units_add(this_object, other_object, op_string) 132 else: 133 if not inp.units.is_dimensionless:--> 134 raise YTUnitOperationError(op_string, inp.units, dimensionless) 135 return ret 136 YTUnitOperationError: The subtraction operator for YTArrays with units (keV) and (1) is not well defined. RegardsAlex From: jzuhone@gmail.com Date: Tue, 1 Sep 2015 09:35:20 -0400 To: yt-users@lists.spacepope.org Subject: Re: [yt-users] problem with units Hi Alex, Ok, so this actually makes things a bit simpler. You have one of two options. You can install one of our nightly development packages. The upside to this is that you will get the bugfix that was recently applied. The downside to this is that you will also get experimental changes that have been merged in lately, which may be unstable. If you want to install this version, you can use this command: conda install -c https://conda.binstar.org/jzuhone/channel/dev yt which will update you to last night’s development version. Alternatively, we will be updating the stable conda package with a bugfix release very soon (maybe in the next week or so), so if you want you can wait for that and I will be sure to let you know when it comes out. Best, John On Sep 1, 2015, at 3:23 AM, alex volioths <alex-volos@hotmail.com> wrote:Hi John, thank you for your time and help. I used conda to install yt. I am using Ubuntu 14 LTS but I am a newbie. Again, thank you. Alex From: jzuhone@gmail.com Date: Mon, 31 Aug 2015 17:49:51 -0400 To: yt-users@lists.spacepope.org Subject: Re: [yt-users] problem with units Hi Alex, Sorry—the delays on my end are longer than yours. We’ve fixed this bug, but I’m still a little unclear as to how you installed yt. You’re using spyder to run the script, but I don’t think you can install yt using spyder, so you must have used “pip install yt” to install it, or maybe you installed it from source. Do you remember how you did it? Also, is this Linux or Mac OS X? Best, John On Aug 29, 2015, at 1:28 PM, alex volioths <alex-volos@hotmail.com> wrote:Hi John, I am sorry for the late reply. I use spyder which comes with modules installed. Thank you for your help! Alex From: jzuhone@gmail.com Date: Wed, 26 Aug 2015 17:50:44 -0400 To: yt-users@lists.spacepope.org Subject: Re: [yt-users] problem with units Alex, My apologies—this is a bug in the code. I have a fix, which I hope to have ready by tonight or tomorrow. Just a quick question—how did you install yt? It looks like your Python stack is in /usr/local. Best, John On Aug 26, 2015, at 3:26 AM, alex volioths <alex-volos@hotmail.com> wrote:Hello John I am using spyder to run the script. Spyder is using the 1.8.2 version. CheersAlex From: jzuhone@gmail.com Date: Tue, 25 Aug 2015 09:54:31 -0400 To: yt-users@lists.spacepope.org Subject: Re: [yt-users] problem with units Hi Alex, Sorry for the trouble--I'll see if I can figure out what's gone wrong on this end. It looks like you're running yt 3.2--can you tell me what version of NumPy you are running? Best, John John ZuHone Kavli Center for Astrophysics and Space Research Massachusetts Institute of Technology 77 Massachusetts Ave., 37-582G Cambridge, MA 02139 (w) 617-253-2354 (m) 781-708-5004 jzuhone@space.mit.edu jzuhone@gmail.com http://www.jzuhone.com On Aug 25, 2015, at 9:41 AM, alex volioths <alex-volos@hotmail.com> wrote: Hello everyone, I've been practicing with the example "Creating a X-ray observation from an in-memory dataset" from here http://yt-project.org/doc/analyzing/analysis_modules/photon_simulator.html However even with simple copy and paste after defining the photons I get this error message: File "/usr/local/lib/python2.7/dist-packages/spyderlib/widgets/externalshell/sitecustomize.py", line 685, in runfile execfile(filename, namespace) File "/usr/local/lib/python2.7/dist-packages/spyderlib/widgets/externalshell/sitecustomize.py", line 78, in execfile builtins.execfile(filename, *where) File "/home/afi/Documents/X_ray_sim/X_mock.py", line 75, in <module> exp_time, thermal_model, center="c") File "/usr/local/lib/python2.7/dist-packages/yt-3.2-py2.7-linux-x86_64.egg/yt/analysis_modules/photon_simulator/photon_simulator.py", line 330, in from_scratch photons = photon_model(data_source, parameters) File "/usr/local/lib/python2.7/dist-packages/yt-3.2-py2.7-linux-x86_64.egg/yt/analysis_modules/photon_simulator/photon_models.py", line 140, in __call__ kT_bins = np.linspace(kT_min, max(my_kT_max, kT_max), num=n_kT+1) File "/usr/lib/python2.7/dist-packages/numpy/core/function_base.py", line 87, in linspace step = (stop-start)/float((num-1)) File "/usr/local/lib/python2.7/dist-packages/yt-3.2-py2.7-linux-x86_64.egg/yt/units/yt_array.py", line 745, in __sub__ ro = sanitize_units_add(self, right_object, "subtraction") File "/usr/local/lib/python2.7/dist-packages/yt-3.2-py2.7-linux-x86_64.egg/yt/units/yt_array.py", line 134, in sanitize_units_add raise YTUnitOperationError(op_string, inp.units, dimensionless) YTUnitOperationError: The subtraction operator for YTArrays with units (keV) and (1) is not well defined. Any ideas? I am new to yt and i can't see something wrong. Thnak you Alex _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org______________... mailing listyt-users@lists.spacepope.orghttp://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org______________... mailing listyt-users@lists.spacepope.orghttp://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org______________... mailing listyt-users@lists.spacepope.orghttp://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

Hello John, I followed your instructions and run the script from the terminal but I still get this error message: YTUnitOperationError Traceback (most recent call last)/home/afi/Documents/X_ray_sim/X_mock.py in <module>() 74 75 photons = PhotonList.from_scratch(sphere, redshift, A,---> 76 exp_time, thermal_model, center="c") 77 78 /home/afi/miniconda/lib/python2.7/site-packages/yt/analysis_modules/photon_simulator/photon_simulator.pyc in from_scratch(cls, data_source, redshift, area, exp_time, photon_model, parameters, center, dist, cosmology) 328 parameters["Width"] = 2.*width.in_units("kpc") 329 --> 330 photons = photon_model(data_source, parameters) 331 332 mylog.info("Finished generating photons.") /home/afi/miniconda/lib/python2.7/site-packages/yt/analysis_modules/photon_simulator/photon_models.pyc in __call__(self, data_source, parameters) 138 idxs = np.argsort(kT) 139 --> 140 kT_bins = np.linspace(kT_min, max(my_kT_max, kT_max), num=n_kT+1) 141 dkT = kT_bins[1]-kT_bins[0] 142 kT_idxs = np.digitize(kT[idxs], kT_bins) /home/afi/miniconda/lib/python2.7/site-packages/numpy/core/function_base.pyc in linspace(start, stop, num, endpoint, retstep, dtype) 96 if num == 1: 97 return array([start], dtype=dtype)---> 98 step = (stop-start)/float((num-1)) 99 y = _nx.arange(0, num, dtype=dtype) * step + start 100 y[-1] = stop /home/afi/miniconda/lib/python2.7/site-packages/yt/units/yt_array.pyc in __sub__(self, right_object) 743 744 """--> 745 ro = sanitize_units_add(self, right_object, "subtraction") 746 return YTArray(super(YTArray, self).__sub__(ro)) 747 /home/afi/miniconda/lib/python2.7/site-packages/yt/units/yt_array.pyc in sanitize_units_add(this_object, other_object, op_string) 132 else: 133 if not inp.units.is_dimensionless:--> 134 raise YTUnitOperationError(op_string, inp.units, dimensionless) 135 return ret 136 YTUnitOperationError: The subtraction operator for YTArrays with units (keV) and (1) is not well defined. CheersAlex From: jzuhone@gmail.com Date: Tue, 1 Sep 2015 11:41:30 -0400 To: yt-users@lists.spacepope.org Subject: Re: [yt-users] problem with units Hi Alex, It appears that Conda is not recognizing the development version as newer than yours. I’ll need to look into why that is, but in the meantime you can do the following: conda remove ytconda install -c https://conda.binstar.org/jzuhone/channel/dev yt This should take care of it—if not, let me know. Best, John On Sep 1, 2015, at 11:34 AM, alex volioths <alex-volos@hotmail.com> wrote:Hello John, I decided to upgrade now to give some feedback that could be useful. After the update command I get: Fetching package metadata: ......Solving package specifications: .# All requested packages already installed.# packages in environment at /home/afi/miniconda:#yt 3.2 np19py27_0 when I run the script from the terminal and not from spyder I get this warning: YTUnitOperationError Traceback (most recent call last)/home/afi/Documents/X_ray_sim/X_mock.py in <module>() 73 74 photons = PhotonList.from_scratch(sphere, redshift, A,---> 75 exp_time, thermal_model, center="c") 76 77 /home/afi/miniconda/lib/python2.7/site-packages/yt/analysis_modules/photon_simulator/photon_simulator.pyc in from_scratch(cls, data_source, redshift, area, exp_time, photon_model, parameters, center, dist, cosmology) 328 parameters["Width"] = 2.*width.in_units("kpc") 329 --> 330 photons = photon_model(data_source, parameters) 331 332 mylog.info("Finished generating photons.") /home/afi/miniconda/lib/python2.7/site-packages/yt/analysis_modules/photon_simulator/photon_models.pyc in __call__(self, data_source, parameters) 138 idxs = np.argsort(kT) 139 --> 140 kT_bins = np.linspace(kT_min, max(my_kT_max, kT_max), num=n_kT+1) 141 dkT = kT_bins[1]-kT_bins[0] 142 kT_idxs = np.digitize(kT[idxs], kT_bins) /home/afi/miniconda/lib/python2.7/site-packages/numpy/core/function_base.pyc in linspace(start, stop, num, endpoint, retstep, dtype) 96 if num == 1: 97 return array([start], dtype=dtype)---> 98 step = (stop-start)/float((num-1)) 99 y = _nx.arange(0, num, dtype=dtype) * step + start 100 y[-1] = stop /home/afi/miniconda/lib/python2.7/site-packages/yt/units/yt_array.pyc in __sub__(self, right_object) 743 744 """--> 745 ro = sanitize_units_add(self, right_object, "subtraction") 746 return YTArray(super(YTArray, self).__sub__(ro)) 747 /home/afi/miniconda/lib/python2.7/site-packages/yt/units/yt_array.pyc in sanitize_units_add(this_object, other_object, op_string) 132 else: 133 if not inp.units.is_dimensionless:--> 134 raise YTUnitOperationError(op_string, inp.units, dimensionless) 135 return ret 136 YTUnitOperationError: The subtraction operator for YTArrays with units (keV) and (1) is not well defined. RegardsAlex From: jzuhone@gmail.com Date: Tue, 1 Sep 2015 09:35:20 -0400 To: yt-users@lists.spacepope.org Subject: Re: [yt-users] problem with units Hi Alex, Ok, so this actually makes things a bit simpler. You have one of two options. You can install one of our nightly development packages. The upside to this is that you will get the bugfix that was recently applied. The downside to this is that you will also get experimental changes that have been merged in lately, which may be unstable. If you want to install this version, you can use this command: conda install -c https://conda.binstar.org/jzuhone/channel/dev yt which will update you to last night’s development version. Alternatively, we will be updating the stable conda package with a bugfix release very soon (maybe in the next week or so), so if you want you can wait for that and I will be sure to let you know when it comes out. Best, John On Sep 1, 2015, at 3:23 AM, alex volioths <alex-volos@hotmail.com> wrote:Hi John, thank you for your time and help. I used conda to install yt. I am using Ubuntu 14 LTS but I am a newbie. Again, thank you. Alex From: jzuhone@gmail.com Date: Mon, 31 Aug 2015 17:49:51 -0400 To: yt-users@lists.spacepope.org Subject: Re: [yt-users] problem with units Hi Alex, Sorry—the delays on my end are longer than yours. We’ve fixed this bug, but I’m still a little unclear as to how you installed yt. You’re using spyder to run the script, but I don’t think you can install yt using spyder, so you must have used “pip install yt” to install it, or maybe you installed it from source. Do you remember how you did it? Also, is this Linux or Mac OS X? Best, John On Aug 29, 2015, at 1:28 PM, alex volioths <alex-volos@hotmail.com> wrote:Hi John, I am sorry for the late reply. I use spyder which comes with modules installed. Thank you for your help! Alex From: jzuhone@gmail.com Date: Wed, 26 Aug 2015 17:50:44 -0400 To: yt-users@lists.spacepope.org Subject: Re: [yt-users] problem with units Alex, My apologies—this is a bug in the code. I have a fix, which I hope to have ready by tonight or tomorrow. Just a quick question—how did you install yt? It looks like your Python stack is in /usr/local. Best, John On Aug 26, 2015, at 3:26 AM, alex volioths <alex-volos@hotmail.com> wrote:Hello John I am using spyder to run the script. Spyder is using the 1.8.2 version. CheersAlex From: jzuhone@gmail.com Date: Tue, 25 Aug 2015 09:54:31 -0400 To: yt-users@lists.spacepope.org Subject: Re: [yt-users] problem with units Hi Alex, Sorry for the trouble--I'll see if I can figure out what's gone wrong on this end. It looks like you're running yt 3.2--can you tell me what version of NumPy you are running? Best, John John ZuHone Kavli Center for Astrophysics and Space Research Massachusetts Institute of Technology 77 Massachusetts Ave., 37-582G Cambridge, MA 02139 (w) 617-253-2354 (m) 781-708-5004 jzuhone@space.mit.edu jzuhone@gmail.com http://www.jzuhone.com On Aug 25, 2015, at 9:41 AM, alex volioths <alex-volos@hotmail.com> wrote: Hello everyone, I've been practicing with the example "Creating a X-ray observation from an in-memory dataset" from here http://yt-project.org/doc/analyzing/analysis_modules/photon_simulator.html However even with simple copy and paste after defining the photons I get this error message: File "/usr/local/lib/python2.7/dist-packages/spyderlib/widgets/externalshell/sitecustomize.py", line 685, in runfile execfile(filename, namespace) File "/usr/local/lib/python2.7/dist-packages/spyderlib/widgets/externalshell/sitecustomize.py", line 78, in execfile builtins.execfile(filename, *where) File "/home/afi/Documents/X_ray_sim/X_mock.py", line 75, in <module> exp_time, thermal_model, center="c") File "/usr/local/lib/python2.7/dist-packages/yt-3.2-py2.7-linux-x86_64.egg/yt/analysis_modules/photon_simulator/photon_simulator.py", line 330, in from_scratch photons = photon_model(data_source, parameters) File "/usr/local/lib/python2.7/dist-packages/yt-3.2-py2.7-linux-x86_64.egg/yt/analysis_modules/photon_simulator/photon_models.py", line 140, in __call__ kT_bins = np.linspace(kT_min, max(my_kT_max, kT_max), num=n_kT+1) File "/usr/lib/python2.7/dist-packages/numpy/core/function_base.py", line 87, in linspace step = (stop-start)/float((num-1)) File "/usr/local/lib/python2.7/dist-packages/yt-3.2-py2.7-linux-x86_64.egg/yt/units/yt_array.py", line 745, in __sub__ ro = sanitize_units_add(self, right_object, "subtraction") File "/usr/local/lib/python2.7/dist-packages/yt-3.2-py2.7-linux-x86_64.egg/yt/units/yt_array.py", line 134, in sanitize_units_add raise YTUnitOperationError(op_string, inp.units, dimensionless) YTUnitOperationError: The subtraction operator for YTArrays with units (keV) and (1) is not well defined. Any ideas? I am new to yt and i can't see something wrong. Thnak you Alex _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org______________... mailing listyt-users@lists.spacepope.orghttp://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org______________... mailing listyt-users@lists.spacepope.orghttp://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org______________... mailing listyt-users@lists.spacepope.orghttp://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org _______________________________________________ yt-users mailing list yt-users@lists.spacepope.orghttp://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org______________... mailing listyt-users@lists.spacepope.orghttp://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

Hi John, it says: yt 3.2 np19py27_0 RegardsAlex From: jzuhone@gmail.com Date: Thu, 3 Sep 2015 09:29:53 -0400 To: yt-users@lists.spacepope.org Subject: Re: [yt-users] problem with units Hi Alex, If you type conda list yt what does it say? Check the last few lines at the bottom since it will print the name of any package with the letters “yt” in it. John On Sep 2, 2015, at 4:55 AM, alex volioths <alex-volos@hotmail.com> wrote:Hello John, I followed your instructions and run the script from the terminal but I still get this error message: YTUnitOperationError Traceback (most recent call last)/home/afi/Documents/X_ray_sim/X_mock.py in <module>() 74 75 photons = PhotonList.from_scratch(sphere, redshift, A,---> 76 exp_time, thermal_model, center="c") 77 78 /home/afi/miniconda/lib/python2.7/site-packages/yt/analysis_modules/photon_simulator/photon_simulator.pyc in from_scratch(cls, data_source, redshift, area, exp_time, photon_model, parameters, center, dist, cosmology) 328 parameters["Width"] = 2.*width.in_units("kpc") 329 --> 330 photons = photon_model(data_source, parameters) 331 332 mylog.info("Finished generating photons.") /home/afi/miniconda/lib/python2.7/site-packages/yt/analysis_modules/photon_simulator/photon_models.pyc in __call__(self, data_source, parameters) 138 idxs = np.argsort(kT) 139 --> 140 kT_bins = np.linspace(kT_min, max(my_kT_max, kT_max), num=n_kT+1) 141 dkT = kT_bins[1]-kT_bins[0] 142 kT_idxs = np.digitize(kT[idxs], kT_bins) /home/afi/miniconda/lib/python2.7/site-packages/numpy/core/function_base.pyc in linspace(start, stop, num, endpoint, retstep, dtype) 96 if num == 1: 97 return array([start], dtype=dtype)---> 98 step = (stop-start)/float((num-1)) 99 y = _nx.arange(0, num, dtype=dtype) * step + start 100 y[-1] = stop /home/afi/miniconda/lib/python2.7/site-packages/yt/units/yt_array.pyc in __sub__(self, right_object) 743 744 """--> 745 ro = sanitize_units_add(self, right_object, "subtraction") 746 return YTArray(super(YTArray, self).__sub__(ro)) 747 /home/afi/miniconda/lib/python2.7/site-packages/yt/units/yt_array.pyc in sanitize_units_add(this_object, other_object, op_string) 132 else: 133 if not inp.units.is_dimensionless:--> 134 raise YTUnitOperationError(op_string, inp.units, dimensionless) 135 return ret 136 YTUnitOperationError: The subtraction operator for YTArrays with units (keV) and (1) is not well defined. CheersAlex From: jzuhone@gmail.com Date: Tue, 1 Sep 2015 11:41:30 -0400 To: yt-users@lists.spacepope.org Subject: Re: [yt-users] problem with units Hi Alex, It appears that Conda is not recognizing the development version as newer than yours. I’ll need to look into why that is, but in the meantime you can do the following: conda remove ytconda install -c https://conda.binstar.org/jzuhone/channel/dev yt This should take care of it—if not, let me know. Best, John On Sep 1, 2015, at 11:34 AM, alex volioths <alex-volos@hotmail.com> wrote:Hello John, I decided to upgrade now to give some feedback that could be useful. After the update command I get: Fetching package metadata: ......Solving package specifications: .# All requested packages already installed.# packages in environment at /home/afi/miniconda:#yt 3.2 np19py27_0 when I run the script from the terminal and not from spyder I get this warning: YTUnitOperationError Traceback (most recent call last)/home/afi/Documents/X_ray_sim/X_mock.py in <module>() 73 74 photons = PhotonList.from_scratch(sphere, redshift, A,---> 75 exp_time, thermal_model, center="c") 76 77 /home/afi/miniconda/lib/python2.7/site-packages/yt/analysis_modules/photon_simulator/photon_simulator.pyc in from_scratch(cls, data_source, redshift, area, exp_time, photon_model, parameters, center, dist, cosmology) 328 parameters["Width"] = 2.*width.in_units("kpc") 329 --> 330 photons = photon_model(data_source, parameters) 331 332 mylog.info("Finished generating photons.") /home/afi/miniconda/lib/python2.7/site-packages/yt/analysis_modules/photon_simulator/photon_models.pyc in __call__(self, data_source, parameters) 138 idxs = np.argsort(kT) 139 --> 140 kT_bins = np.linspace(kT_min, max(my_kT_max, kT_max), num=n_kT+1) 141 dkT = kT_bins[1]-kT_bins[0] 142 kT_idxs = np.digitize(kT[idxs], kT_bins) /home/afi/miniconda/lib/python2.7/site-packages/numpy/core/function_base.pyc in linspace(start, stop, num, endpoint, retstep, dtype) 96 if num == 1: 97 return array([start], dtype=dtype)---> 98 step = (stop-start)/float((num-1)) 99 y = _nx.arange(0, num, dtype=dtype) * step + start 100 y[-1] = stop /home/afi/miniconda/lib/python2.7/site-packages/yt/units/yt_array.pyc in __sub__(self, right_object) 743 744 """--> 745 ro = sanitize_units_add(self, right_object, "subtraction") 746 return YTArray(super(YTArray, self).__sub__(ro)) 747 /home/afi/miniconda/lib/python2.7/site-packages/yt/units/yt_array.pyc in sanitize_units_add(this_object, other_object, op_string) 132 else: 133 if not inp.units.is_dimensionless:--> 134 raise YTUnitOperationError(op_string, inp.units, dimensionless) 135 return ret 136 YTUnitOperationError: The subtraction operator for YTArrays with units (keV) and (1) is not well defined. RegardsAlex From: jzuhone@gmail.com Date: Tue, 1 Sep 2015 09:35:20 -0400 To: yt-users@lists.spacepope.org Subject: Re: [yt-users] problem with units Hi Alex, Ok, so this actually makes things a bit simpler. You have one of two options. You can install one of our nightly development packages. The upside to this is that you will get the bugfix that was recently applied. The downside to this is that you will also get experimental changes that have been merged in lately, which may be unstable. If you want to install this version, you can use this command: conda install -c https://conda.binstar.org/jzuhone/channel/dev yt which will update you to last night’s development version. Alternatively, we will be updating the stable conda package with a bugfix release very soon (maybe in the next week or so), so if you want you can wait for that and I will be sure to let you know when it comes out. Best, John On Sep 1, 2015, at 3:23 AM, alex volioths <alex-volos@hotmail.com> wrote:Hi John, thank you for your time and help. I used conda to install yt. I am using Ubuntu 14 LTS but I am a newbie. Again, thank you. Alex From: jzuhone@gmail.com Date: Mon, 31 Aug 2015 17:49:51 -0400 To: yt-users@lists.spacepope.org Subject: Re: [yt-users] problem with units Hi Alex, Sorry—the delays on my end are longer than yours. We’ve fixed this bug, but I’m still a little unclear as to how you installed yt. You’re using spyder to run the script, but I don’t think you can install yt using spyder, so you must have used “pip install yt” to install it, or maybe you installed it from source. Do you remember how you did it? Also, is this Linux or Mac OS X? Best, John On Aug 29, 2015, at 1:28 PM, alex volioths <alex-volos@hotmail.com> wrote:Hi John, I am sorry for the late reply. I use spyder which comes with modules installed. Thank you for your help! Alex From: jzuhone@gmail.com Date: Wed, 26 Aug 2015 17:50:44 -0400 To: yt-users@lists.spacepope.org Subject: Re: [yt-users] problem with units Alex, My apologies—this is a bug in the code. I have a fix, which I hope to have ready by tonight or tomorrow. Just a quick question—how did you install yt? It looks like your Python stack is in /usr/local. Best, John On Aug 26, 2015, at 3:26 AM, alex volioths <alex-volos@hotmail.com> wrote:Hello John I am using spyder to run the script. Spyder is using the 1.8.2 version. CheersAlex From: jzuhone@gmail.com Date: Tue, 25 Aug 2015 09:54:31 -0400 To: yt-users@lists.spacepope.org Subject: Re: [yt-users] problem with units Hi Alex, Sorry for the trouble--I'll see if I can figure out what's gone wrong on this end. It looks like you're running yt 3.2--can you tell me what version of NumPy you are running? Best, John John ZuHone Kavli Center for Astrophysics and Space Research Massachusetts Institute of Technology 77 Massachusetts Ave., 37-582G Cambridge, MA 02139 (w) 617-253-2354 (m) 781-708-5004 jzuhone@space.mit.edu jzuhone@gmail.com http://www.jzuhone.com On Aug 25, 2015, at 9:41 AM, alex volioths <alex-volos@hotmail.com> wrote: Hello everyone, I've been practicing with the example "Creating a X-ray observation from an in-memory dataset" from here http://yt-project.org/doc/analyzing/analysis_modules/photon_simulator.html However even with simple copy and paste after defining the photons I get this error message: File "/usr/local/lib/python2.7/dist-packages/spyderlib/widgets/externalshell/sitecustomize.py", line 685, in runfile execfile(filename, namespace) File "/usr/local/lib/python2.7/dist-packages/spyderlib/widgets/externalshell/sitecustomize.py", line 78, in execfile builtins.execfile(filename, *where) File "/home/afi/Documents/X_ray_sim/X_mock.py", line 75, in <module> exp_time, thermal_model, center="c") File "/usr/local/lib/python2.7/dist-packages/yt-3.2-py2.7-linux-x86_64.egg/yt/analysis_modules/photon_simulator/photon_simulator.py", line 330, in from_scratch photons = photon_model(data_source, parameters) File "/usr/local/lib/python2.7/dist-packages/yt-3.2-py2.7-linux-x86_64.egg/yt/analysis_modules/photon_simulator/photon_models.py", line 140, in __call__ kT_bins = np.linspace(kT_min, max(my_kT_max, kT_max), num=n_kT+1) File "/usr/lib/python2.7/dist-packages/numpy/core/function_base.py", line 87, in linspace step = (stop-start)/float((num-1)) File "/usr/local/lib/python2.7/dist-packages/yt-3.2-py2.7-linux-x86_64.egg/yt/units/yt_array.py", line 745, in __sub__ ro = sanitize_units_add(self, right_object, "subtraction") File "/usr/local/lib/python2.7/dist-packages/yt-3.2-py2.7-linux-x86_64.egg/yt/units/yt_array.py", line 134, in sanitize_units_add raise YTUnitOperationError(op_string, inp.units, dimensionless) YTUnitOperationError: The subtraction operator for YTArrays with units (keV) and (1) is not well defined. Any ideas? I am new to yt and i can't see something wrong. Thnak you Alex _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org______________... mailing listyt-users@lists.spacepope.orghttp://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org______________... mailing listyt-users@lists.spacepope.orghttp://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org______________... mailing listyt-users@lists.spacepope.orghttp://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org _______________________________________________ yt-users mailing list yt-users@lists.spacepope.orghttp://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org______________... mailing listyt-users@lists.spacepope.orghttp://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org______________... mailing listyt-users@lists.spacepope.orghttp://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org