Hmmm, that would have been useful. Numpy 1.6.2 has the percentile function too, oh well. Maybe the best would be to add a new function to lib.statistics? Something like the scipy function:
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.scoreatpercentile.html#scipy.stats.scoreatpercentile or: http://code.activestate.com/recipes/511478-finding-the-percentile-of-the-values/ Licencing prevents us copying such code. Or maybe a simple algorithm could be created: - Create a sorted list of chi2. - The 90% value would be the value at the index int(0.9 * N). - The 50% value would be the value at the index int(0.5 * N). - The 20% value would be the value at the index int(0.2 * N). - The 10% value would be the value at the index int(0.1 * N). There are not really percentiles, but for this OpenDX map it might be good enough. Regards, Edward On 9 May 2014 18:35, Troels Emtekær Linnet <[email protected]> wrote: > Hm. > > You need numpy 1.9 > http://docs.scipy.org/doc/numpy-dev/release.html > > I have 1.4 > > 2014-05-09 18:21 GMT+02:00 Edward d'Auvergne <[email protected]>: >> Here is a demo: >> >> """ >> from numpy import array, float64, percentile >> >> a = array(range(100001), float64) >> print(percentile(a, 90)) >> print(percentile(a, 50)) >> print(percentile(a, 20)) >> print(percentile(a, 10)) >> """ >> >> Regards, >> >> Edward >> >> >> >> On 9 May 2014 18:14, Edward d'Auvergne <[email protected]> wrote: >>> You may also want to try this logic: >>> >>> """ >>> from numpy import percentile >>> >>> all_chi2 = array(all_chi2, float64) >>> self.contour_levels = [] >>> self.contour_levels.append(percentile(all_chi2, 90)) >>> self.contour_levels.append(percentile(all_chi2, 50)) >>> self.contour_levels.append(percentile(all_chi2, 20)) >>> self.contour_levels.append(percentile(all_chi2, 10)) >>> """ >>> >>> This might work better with OpenDX. >>> >>> Regards, >>> >>> Edward >>> >>> >>> >>> >>> On 9 May 2014 18:08, Edward d'Auvergne <[email protected]> wrote: >>>> Hi Troels, >>>> >>>> A better way to handle this would be to pass in an array of 4 values >>>> for the isosurface levels into write_program(). Then you can change >>>> these values as needed in pipe_control.opendx and not have to worry >>>> about what happens in lib.software.opendx ever again. It would >>>> decouple the logic and be much more flexible. >>>> >>>> Regards, >>>> >>>> Edward >>>> >>>> On 9 May 2014 17:33, <[email protected]> wrote: >>>>> Author: tlinnet >>>>> Date: Fri May 9 17:33:05 2014 >>>>> New Revision: 23132 >>>>> >>>>> URL: http://svn.gna.org/viewcvs/relax?rev=23132&view=rev >>>>> Log: >>>>> Made collecting of min, max and median value of chi2, when creating the >>>>> chi2 map. >>>>> >>>>> task #7792: (https://gna.org/task/?7792) Make the dx.map write suggest >>>>> chi surface values. >>>>> >>>>> Modified: >>>>> trunk/pipe_control/opendx.py >>>>> >>>>> Modified: trunk/pipe_control/opendx.py >>>>> URL: >>>>> http://svn.gna.org/viewcvs/relax/trunk/pipe_control/opendx.py?rev=23132&r1=23131&r2=23132&view=diff >>>>> ============================================================================== >>>>> --- trunk/pipe_control/opendx.py (original) >>>>> +++ trunk/pipe_control/opendx.py Fri May 9 17:33:05 2014 >>>>> @@ -24,7 +24,7 @@ >>>>> >>>>> >>>>> # Python module imports. >>>>> -from numpy import float64, array, zeros >>>>> +from numpy import float64, array, median, zeros >>>>> from time import asctime, localtime >>>>> >>>>> # relax module imports. >>>>> @@ -164,8 +164,11 @@ >>>>> # Create the strings associated with the map axes. >>>>> self.map_axes() >>>>> >>>>> + # Generate the map. >>>>> + self.create_map() >>>>> + >>>>> # Create the OpenDX .net program file. >>>>> - write_program(file_prefix=self.file_prefix, >>>>> point_file=self.point_file, dir=self.dir, inc=self.inc, N=self.n, >>>>> num_points=self.num_points, labels=self.labels, >>>>> tick_locations=self.tick_locations, tick_values=self.tick_values, >>>>> date=self.date) >>>>> + write_program(file_prefix=self.file_prefix, >>>>> point_file=self.point_file, dir=self.dir, inc=self.inc, N=self.n, >>>>> num_points=self.num_points, labels=self.labels, >>>>> tick_locations=self.tick_locations, tick_values=self.tick_values, >>>>> date=self.date, min_chi2=self.min_chi2, max_chi2=self.max_chi2, >>>>> median_chi2=self.median_chi2) >>>>> >>>>> # Create the OpenDX .cfg program configuration file. >>>>> write_config(file_prefix=self.file_prefix, dir=self.dir, >>>>> date=self.date) >>>>> @@ -176,9 +179,6 @@ >>>>> # Create the OpenDX .general and data files for the given point. >>>>> if self.num_points > 1: >>>>> write_point(file_prefix=self.point_file, dir=self.dir, >>>>> inc=self.inc, point=self.point, num_points=self.num_points, >>>>> bounds=self.bounds, N=self.n) >>>>> - >>>>> - # Generate the map. >>>>> - self.create_map() >>>>> >>>>> >>>>> def create_map(self): >>>>> @@ -211,6 +211,11 @@ >>>>> percent = 0.0 >>>>> percent_inc = 100.0 / (self.inc + 1.0)**(self.n - 1.0) >>>>> print("%-10s%8.3f%-1s" % ("Progress:", percent, "%")) >>>>> + >>>>> + # Define min/max chi2 values. >>>>> + min_chi2 = 1e20 >>>>> + max_chi2 = 1. >>>>> + all_chi = [] >>>>> >>>>> # Fix the diffusion tensor. >>>>> unfix = False >>>>> @@ -257,6 +262,14 @@ >>>>> else: >>>>> map_file.write("%30f\n" % chi2) >>>>> >>>>> + # Save min and max values of chi2. >>>>> + all_chi.append(chi2) >>>>> + if chi2 < min_chi2: >>>>> + min_chi2 = chi2 >>>>> + >>>>> + if chi2 > max_chi2: >>>>> + max_chi2 = chi2 >>>>> + >>>>> # Increment the value of the third parameter. >>>>> values[2] = values[2] + self.step_size[2] >>>>> >>>>> @@ -274,6 +287,11 @@ >>>>> if unfix: >>>>> cdp.diff_tensor.fixed = False >>>>> >>>>> + # Save the min/max chi2 values. >>>>> + self.min_chi2 = min_chi2 >>>>> + self.max_chi2 = max_chi2 >>>>> + # Save the median chi2 value. >>>>> + self.median_chi2 = median(array(all_chi)) >>>>> >>>>> def map_axes(self): >>>>> """Function for creating labels, tick locations, and tick values >>>>> for an OpenDX map.""" >>>>> >>>>> >>>>> _______________________________________________ >>>>> relax (http://www.nmr-relax.com) >>>>> >>>>> This is the relax-commits mailing list >>>>> [email protected] >>>>> >>>>> To unsubscribe from this list, get a password >>>>> reminder, or change your subscription options, >>>>> visit the list information page at >>>>> https://mail.gna.org/listinfo/relax-commits >> >> _______________________________________________ >> relax (http://www.nmr-relax.com) >> >> This is the relax-devel mailing list >> [email protected] >> >> To unsubscribe from this list, get a password >> reminder, or change your subscription options, >> visit the list information page at >> https://mail.gna.org/listinfo/relax-devel _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
