yes, correct. 64 bit Mountain Lion with 64 bit Anaconda. Am Freitag, 13. Juni 2014 09:11:56 UTC+2 schrieb Thomas: But you are running OSX 64-bit with anaconda 64-bit, right? On Wed, Jun 11, 2014 at 1:54 PM, <stein...@gmail.com> wrote:
Hi Thomas, thanks for the quick reply. There is a little misunderstanding though: I'm trying to get hddm working on OSX mountain lion (10.8.5) for which there is no 32 bit version.
It's these error messages, that I was referring to:
"""""""" 1.pip install -U pymc
Command /Applications/anaconda/bin/python -c "import setuptools, tokenize;__file__='/private/var/folders/vf/zy_t4gd13831lkzwvkq1qk6m0000gn/T/pip_build_qiangshen/pymc/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /var/folders/vf/zy_t4gd13831lkzwvkq1qk6m0000gn/T/pip-HYXzxx-record/install-record.txt --single-version-externally-managed --compile failed with error code 1 in /private/var/folders/vf/zy_t4gd13831lkzwvkq1qk6m0000gn/T/pip_build_qiangshen/pymc
Storing debug log for failure in /Users/qiangshen/.pip/pip.log
2. pip install -U kabuki
Command python setup.py egg_info failed with error code 1 in /private/var/folders/vf/zy_t4gd13831lkzwvkq1qk6m0000gn/T/pip_build_qiangshen/kabuki
Storing debug log for failure in /Users/qiangshen/.pip/pip.log
3. pip install -U hddm
Command python setup.py egg_info failed with error code 1 in /private/var/folders/vf/zy_t4gd13831lkzwvkq1qk6m0000gn/T/pip_build_qiangshen/hddm
Storing debug log for failure in /Users/qiangshen/.pip/pip.log
""""""
So I suppose I need to install a Fortran compiler now?
Cheers, Benjamin Am Mittwoch, 11. Juni 2014 12:51:25 UTC+2 schrieb Thomas:
Hi Benjamin,
A user posted windows build instructions in another thread: " I wanted to install HDDM on a windows
machine but was riddled with either DLL or MS visual studio errors,
especially with PyMC. I tried clean python install and also Anaconda
with no luck. Here is a procedure that worked for me so thought maybe I
will post it here in case people are still looking for a solution. As
the procedure depends on MinGW32 please make sure that you install
everything 32 bit even though your Windows is 64 bit. You need admin rights to do many of the following. 1. Install Python 2.7.6 32 bit. Lets call the install directory path_to_Python27.
2. Get Numpy and Scipy 2.7 32 bit installers from their websites and install. 3. Install setuptools and pip (32 bit) from http://www.lfd.uci.edu/~gohlke/pythonlibs/
4. Install MinGW32 and append the corresponding bin folder to your environments PATH variable. You can get MinGW32 here http://sourceforge.net/projects/mingw/files/
5. Create file: path_to_Python27\Lib\ distutils\distutils.cfg and put following two lines in there:
[build] compiler=mingw32
6.
Start "cmd" and run following commands in the path_to_Python27\scripts
directory (make sure that you dont have any python instances running)
pip install matplotlib pip install pymc pip install pandas pip install kabuki pip install hddm "
See if that helps. Otherwise I should update the conda windows packages soon.
Thomas
On Wed, Jun 11, 2014 at 12:31 PM, <stein...@gmail.com> wrote:
Hi Quiang,
did you find a solution? I'm stuck precisely where you have been. Any hints on where to get the right compiler or how to work around the Fortran compiler problem?
Thanks a lot, Benjamin Am Sonntag, 8. Juni 2014 03:39:21 UTC+2 schrieb Qiang Shen:
Hi Thomas,
I figured it out, it needs a Fortran compiler which is not available in the original OSX. Thank you all the same.
best wishes,
Qiang On Saturday, June 7, 2014 11:19:37 PM UTC+8, Thomas wrote:
Can you paste the full error log?
On Sat, Jun 7, 2014 at 5:13 PM, Qiang Shen <johns...@gmail.com> wrote:
Do you know how to fix this? Thanks.
On Saturday, June 7, 2014 11:07:12 PM UTC+8, Qiang Shen wrote:
Hi Thomas,
Recently I moved to a new place and need to install the HDDM again on Mac. But I failed to install it correctly. I have tried Anaconda 1.9.2 and Anaconda 2.0.0. Below are the error information.
1.pip install -U pymc
Command /Applications/anaconda/bin/python -c "import setuptools, tokenize;__file__='/private/var/folders/vf/zy_t4gd13831lkzwvkq1qk6m0000gn/T/pip_build_qiangshen/pymc/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /var/folders/vf/zy_t4gd13831lkzwvkq1qk6m0000gn/T/pip-HYXzxx-record/install-record.txt --single-version-externally-managed --compile failed with error code 1 in /private/var/folders/vf/zy_t4gd13831lkzwvkq1qk6m0000gn/T/pip_build_qiangshen/pymc
Storing debug log for failure in /Users/qiangshen/.pip/pip.log
2. pip install -U kabuki
Command python setup.py egg_info failed with error code 1 in /private/var/folders/vf/zy_t4gd13831lkzwvkq1qk6m0000gn/T/pip_build_qiangshen/kabuki
Storing debug log for failure in /Users/qiangshen/.pip/pip.log
3. pip install -U hddm
Command python setup.py egg_info failed with error code 1 in /private/var/folders/vf/zy_t4gd13831lkzwvkq1qk6m0000gn/T/pip_build_qiangshen/hddm
Storing debug log for failure in /Users/qiangshen/.pip/pip.log
On Sunday, June 1, 2014 8:05:37 PM UTC+8, Thomas wrote:
Hi Qiang,
Thanks, I fixed the issues in the tutorial you mentioned.
HDDMRegression should accept a p_outlier keyword argument (e.g. HDDMRegression(data, 'v~x', p_outlier=.05). Does it not?
Thomas On Wed, May 21, 2014 at 9:37 AM, Qiang Shen <johns...@gmail.com> wrote:
Hi Thomas,
In the tutorial, "a_var" should be "a_std",that’s the reasons why it was not listed in the table which should be 4 rows * 8 columns. and also for the posterior plot. In addition, all the plots seem not correctly presented in current version of the tutorial.
For the outlier removal, it is possible to apply it in the with-subject situation? I tested, it seems not work for hddm.HDDMRegressor function. Then how we can make it work in such situation, we have to remove the outliers in advance?
best wishes,
Qiang
On Saturday, May 17, 2014 4:03:36 PM UTC+8, Qiang Shen wrote:
Thanks! Thomas. On Friday, May 16, 2014 7:36:37 AM UTC+8, Thomas wrote: Sorry about that, should be fixed now. Let me know if there are any other problems.
Thomas
On Wed, May 14, 2014 at 12:45 AM, Qiang Shen <johns...@gmail.com> wrote:
Dear Thomas,
I proceed to test the scripts and came across the 2nd error I mentioned to you last time again, see below for details. For the rest of content in the link you sent me, it all works!
hddm.analyze.plot_posterior_nodes([v_WL, v_LL, v_WW])
hddm.analyze.plot_posterior_nodes([v_WL, v_LL, v_WW]) <matplotlib.figure.Figure at 0x10e598590> Traceback (most recent call last):
File "<ipython-input-58-1eee4f977a76>", line 1, in <module> hddm.analyze.plot_posterior_nodes([v_WL, v_LL, v_WW])
File "/Applications/anaconda/lib/python2.7/site-packages/kabuki/analyze.py", line 34, in plot_posterior_nodes
lb = min([min(node.trace()[:]) for node in nodes])
AttributeError: 'float' object has no attribute 'trace'
On Wednesday, May 14, 2014 9:45:56 AM UTC+8, Qiang Shen wrote:
Dear Thomas,
It's so excited that now it works for the following code and I have successfully plotted the attached graph, I'll check whether the following scripts also work on my side. Thanks a lot!
for i, subj_data in data.groupby('subj_idx'):
subj_data.rt.hist(bins=20, histtype='step', ax=ax)
best,
Qiang On Tuesday, May 13, 2014 1:07:33 AM UTC+8, Thomas wrote:
Or were you using hddm_demo.ipynb from the examples directory?
Let me know if that fixes your problems. Thomas On Mon, May 12, 2014 at 12:05 AM, Qiang Shen <johns...@gmail.com> wrote:
Hi Thomas,
Thanks for your reply, initially I haven't import kabuki because it's not mentioned in the tutorial, but after import of kabuki,it's still not work for
for i, subj_data in data.groupby('subj_idx'):
ax.hist(subj_data.rt, bins=20, histtype='step')
Here is the information.
print pymc.__version__ print kabuki.__version__ print hddm.__version__
2.3.2 0.5.4 0.5.3
Traceback (most recent call last):
File "<ipython-input-14-c2c318cf1f63>", line 4, in <module>
ax.hist(subj_data.rt, bins=20, histtype='step')
File "/Applications/anaconda/lib/python2.7/site-packages/matplotlib/axes.py", line 8249, in hist
if isinstance(x, np.ndarray) or not iterable(x[0]):
File "/Applications/anaconda/lib/python2.7/site-packages/pandas/core/series.py", line 491, in __getitem__
result = self.index.get_value(self, key)
File "/Applications/anaconda/lib/python2.7/site-packages/pandas/core/index.py", line 1032, in get_value return self._engine.get_value(s, k)
File "index.pyx", line 97, in pandas.index.IndexEngine.get_value (pandas/index.c:2661)
File "index.pyx", line 105, in pandas.index.IndexEngine.get_value (pandas/index.c:2476)
File "index.pyx", line 149, in pandas.index.IndexEngine.get_loc (pandas/index.c:3215)
File "hashtable.pyx", line 382, in pandas.hashtable.Int64HashTable.get_item (pandas/hashtable.c:6942)
File "hashtable.pyx", line 388, in pandas.hashtable.Int64HashTable.get_item (pandas/hashtable.c:6883)
KeyError: 0
In [15]:
On Sunday, May 11, 2014 8:58:15 PM UTC+8, Thomas wrote:
Hi Qiang,
Windows should make not difference.
Still not sure you have the right versions, can you do:
print pymc.__version__ print kabuki.__version__
print hddm.__version__ After imporiting each module? Dear Thomas,
Do you have any suggestions for the error I mentioned? or it might be better to use Windows for this analysis? Thanks.
best wishes,
Qiang
On Thursday, May 8, 2014 11:14:57 AM UTC+8, Qiang Shen wrote:
Dear Thomas,
Thanks for your reply. The ipython notebook of Anaconda can't be started on my computer and it seem not have a good solution for this. So I tried both ipython-qtconsole and spyder of Anaconda to run the analysis,in general it works smoothly but both can't run the commands I mentioned correctly. Below are the information for my current version of the software, ipython is already the most updated version.
Python 2.7.6 |Anaconda 1.9.2 (x86_64)| (default, Jan 10 2014, 11:23:15) Type "copyright", "credits" or "license" for more information.
IPython 2.0.0 -- An enhanced Interactive Python. ? -> Introduction and overview of IPython's features. %quickref -> Quick reference. help -> Python's own help system.
object? -> Details about 'object', use 'object??' for extra details. %guiref -> A brief reference about the graphical user interface.
best wishes,
Qiang On Wednesday, May 7, 2014 10:26:21 PM UTC+8, Thomas wrote:
Hi Qiang,
Seems like the notebook needs to be updated. Are you using the ipython notebook directly or the website?
Thomas
On Wed, May 7, 2014 at 4:51 AM, Qiang Shen <johns...@gmail.com> wrote:
Hi Thomas,
Thanks, I proceed to try the HDDM, below are the problem I came across so far, do you know why? Does that mean the software is still not correctly installed on my OSX?
1. for i, subj_data in data.groupby('subj_idx'): ax.hist(subj_data.rt, bins=20, histtype='step')
Traceback (most recent call last):
File "<ipython-input-3-3ff08f9d5cbe>", line 2, in <module> ax.hist(subj_data.rt, bins=20, histtype='step')
File "/Applications/anaconda/lib/python2.7/site-packages/matplotlib/axes.py", line 8249, in hist
if isinstance(x, np.ndarray) or not iterable(x[0]):
File "/Applications/anaconda/lib/python2.7/site-packages/pandas/core/series.py", line 491, in __getitem__
result = self.index.get_value(self, key)
File "/Applications/anaconda/lib/python2.7/site-packages/pandas/core/index.py", line 1032, in get_value
return self._engine.get_value(s, k)
File "index.pyx", line 97, in pandas.index.IndexEngine.get_value (pandas/index.c:2661)
File "index.pyx", line 105, in pandas.index.IndexEngine.get_value (pandas/index.c:2476)
File "index.pyx", line 149, in pandas.index.IndexEngine.get_loc (pandas/index.c:3215)
File "hashtable.pyx", line 382, in pandas.hashtable.Int64HashTable.get_item (pandas/hashtable.c:6942)
File "hashtable.pyx", line 388, in pandas.hashtable.Int64HashTable.get_item (pandas/hashtable.c:6883)
KeyError: 0
2.hddm.analyze.plot_posterior_nodes([v_WL, v_LL, v_WW]) <matplotlib.figure.Figure at 0x10ef799d0> Traceback (most recent call last):
File "<ipython-input-13-1eee4f977a76>", line 1, in <module>
hddm.analyze.plot_posterior_nodes([v_WL, v_LL, v_WW])
File "/Applications/anaconda/lib/python2.7/site-packages/kabuki/analyze.py", line 34, in plot_posterior_nodes
lb = min([min(node.trace()[:]) for node in nodes])
AttributeError: 'float' object has no attribute 'trace'
3. m_no_outlier = hddm.HDDMInfo(outlier_data)
m_no_outlier = hddm.HDDMInfo(outlier_data)
Traceback (most recent call last):
File "<ipython-input-25-59a817d0b4fc>", line 1, in <module> m_no_outlier = hddm.HDDMInfo(outlier_data)
AttributeError: 'module' object has no attribute 'HDDMInfo' On Tuesday, May 6, 2014 8:32:02 PM UTC+8, Thomas wrote:
Hi Qiang,
Glad that it's working and thanks for letting us know.
I think there is a problem with the conda package for OSX which we'll have to fix.
Thomas
On Tue, May 6, 2014 at 8:25 AM, Qiang Shen <johns...@gmail.com> wrote:
Hi Thomas,
I have figured out the error after "model = hddm.HDDM(data, depends_on={'v':'difficulty'})". I just updated the software using the command you mentioned in the mailing list, then it's solved!
pip install -U pymc pip install -U kabuki
pip install -U hddm.
Below are the steps I tried for the HDDM instalment on Mac.
1. install anaconda 2. Following instruction, I typed in the terminal the following command. conda install -c pymc pymc conda install -c twiecki hddm After this, the Numpy version is 1.7.1, so I tried "conda install -c pymc pymc" again to link the Numpy to version 1.8.
3. Then I typed pip install -U pymc pip install -U kabuki
pip install -U hddm
On Tuesday, May 6, 2014 10:28:37 AM UTC+8, Qiang Shen wrote:
Hi Thomas,
Here it is. data = hddm.load_csv('simple_difficulty.csv')
model = hddm.HDDM(data, depends_on={'v':'difficulty'})
--------------------------------------------------------------------------- TypeError Traceback (most recent call last)
<ipython-input-20-442fbac9eed4> in <module>()
----> 1 model = hddm.HDDM(data, depends_on={'v':'difficulty'})
/Applications/anaconda/lib/python2.7/site-packages/hddm/models/hddm_info.pyc in __init__(self, *args, **kwargs)
111 self.is_informative = kwargs.pop('informative', True) 112 --> 113 super(HDDM, self).__init__(*args, **kwargs) 114 115 def _create_stochastic_knodes(self, include):
/Applications/anaconda/lib/python2.7/site-packages/hddm/models/base.pyc in __init__(self, data, bias, include, wiener_params, p_outlier, **kwargs)
687 self.wfpt_class = hddm.likelihoods.generate_wfpt_stochastic_class(wp, cdf_range=self.cdf_range)
688 --> 689 super(HDDMBase, self).__init__(data, **kwargs) 690 691 def __getstate__(self):
/Applications/anaconda/lib/python2.7/site-packages/hddm/models/base.pyc in __init__(self, data, **kwargs)
38 self.std_depends = kwargs.pop('std_depends', False) 39 ---> 40 super(AccumulatorModel, self).__init__(data, **kwargs) 41 42
/Applications/anaconda/lib/python2.7/site-packages/kabuki/hierarchical.pyc in __init__(self, data, is_group_model, depends_on, trace_subjs, plot_subjs, plot_var, group_only_nodes)
345 self.db = None 346 --> 347 self._setup_model() 348 349 def _setup_model(self):
/Applications/anaconda/lib/python2.7/site-packages/kabuki/hierarchical.pyc in _setup_model(self)
356 357 # constructs pymc nodes etc and connects them appropriately --> 358 self.create_model() 359 360 def __getstate__(self):
/Applications/anaconda/lib/python2.7/site-packages/kabuki/hierarchical.pyc in create_model(self, max_retries)
426 for tries in range(max_retries):
427 try:
--> 428 _create() 429 except (pm.ZeroProbability, ValueError): 430 continue
/Applications/anaconda/lib/python2.7/site-packages/kabuki/hierarchical.pyc in _create()
422 def _create(): 423 for knode in self.knodes: --> 424 knode.create() 425 426 for tries in range(max_retries):
/Applications/anaconda/lib/python2.7/site-packages/kabuki/hierarchical.pyc in create(self)
165 kwargs['doc'] = node_name
166
--> 167 node = self.create_node(node_name, kwargs, grouped_data) 168 169 if node is not None:
/Applications/anaconda/lib/python2.7/site-packages/kabuki/hierarchical.pyc in create_node(self, node_name, kwargs, data)
173 def create_node(self, node_name, kwargs, data): 174 #actually create the node --> 175 return self.pymc_node(name=node_name, **kwargs) 176
177 def create_tag_and_subj_idx(self, cols, uniq_elem):
/Applications/anaconda/lib/python2.7/site-packages/pymc/distributions.pyc in __init__(self, *args, **kwds)
269 random = debug_wrapper(random)
270 else: --> 271 Stochastic.__init__(self, logp=logp, random=random, logp_partial_gradients = logp_partial_gradients, dtype=dtype, **arg_dict_out) 272
273 new_class.__name__ = name
/Applications/anaconda/lib/python2.7/site-packages/pymc/PyMCObjects.pyc in __init__(self, logp, doc, name, parents, random, trace, value, dtype, rseed, observed, cache_depth, plot, verbose, isdata, check_logp, logp_partial_gradients)
746 dtype=dtype, 747 plot=plot, --> 748 verbose=verbose) 749 750 # self._logp.force_compute()
/Applications/anaconda/lib/python2.7/site-packages/pymc/Node.pyc in __init__(self, doc, name, parents, cache_depth, trace, dtype, plot, verbose)
214 self.extended_children = set()
215 --> 216 Node.__init__(self, doc, name, parents, cache_depth, verbose=verbose) 217 218 if self.dtype is None:
/Applications/anaconda/lib/python2.7/site-packages/pymc/Node.pyc in __init__(self, doc, name, parents, cache_depth, verbose)
125 126 # Initialize --> 127 self.parents = parents 128 129 def _get_parents(self):
/Applications/anaconda/lib/python2.7/site-packages/pymc/Node.pyc in _set_parents(self, new_parents)
148 149 # Get new lazy function --> 150 self.gen_lazy_function() 151 152 parents = property(
/Applications/anaconda/lib/pyt
...
|
|