Hm. License...
2014-05-09 18:56 GMT+02:00 Edward d'Auvergne <[email protected]>: > 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
