Removed 'mean' from carrier_mapper

docker/Dockerfile

@@ -93,10 +93,11 @@ RUN python setup.py install
 WORKDIR ..
 
 #Hammurabi
-RUN git clone https://bitbucket.org/ricphy/hamx -b flexible_output
+RUN git clone https://bitbucket.org/ricphy/hamx -b maintenance
 WORKDIR hamx
 RUN cp install/Makefile ./
 RUN make -f Makefile
+ENV HAMMURABI=/home/Downloads/hamx/bin/hamx
 WORKDIR ..
 
 #IMAGINE

imagine/carrier_mapper.py

@@ -33,12 +33,8 @@ def infinity_mapper(x, a=-np.inf, m=0, b=np.inf):
     return y
 
 
-def unity_mapper(x, a=0, m=0.5, b=1):
+def unity_mapper(x, a=0, b=1):
     """
     Maps x from [0, 1] into the interval [a, b]
     """
-    # rescale and shift
-    if x <= 0.5:
-        return 2*x * (m-a) + a
-    else:
-        return (2*x-1) * (b-m) + m
+    return x * (b-a) + a

imagine/magnetic_fields/magnetic_field/magnetic_field_factory.py

@@ -69,11 +69,11 @@ class MagneticFieldFactory(Loggable, object):
 
     @staticmethod
     def _interval(mean, sigma, n):
-        return [mean-n*sigma, mean, mean+n*sigma]
+        return [mean-n*sigma, mean+n*sigma]
 
     @staticmethod
     def _positive_interval(mean, sigma, n):
-        return [max(0, mean-n*sigma), mean, mean+n*sigma]
+        return [max(0, mean-n*sigma), mean+n*sigma]
 
     @property
     def parameter_defaults(self):
@@ -85,6 +85,15 @@ class MagneticFieldFactory(Loggable, object):
                                         for k, v in new_defaults.items()
                                         if k in self._parameter_defaults)
 
+    @property
+    def variable_defaults(self):
+        variable_defaults = {}
+        for parameter in self.parameter_defaults:
+            low, high = self.variable_to_parameter_mappings[parameter]
+            default = self.parameter_defaults[parameter]
+            variable_defaults[parameter] = (default - low)/(high - low)
+        return variable_defaults
+
     @property
     def variable_to_parameter_mappings(self):
         return self._variable_to_parameter_mappings
@@ -94,7 +103,7 @@ class MagneticFieldFactory(Loggable, object):
         """
         The parameter-mapping must be a dictionary with
         key: parameter-name
-        value: [min, mean, max]
+        value: [min, max]
         """
         for k, v in new_mapping.items():
             if k in self._variable_to_parameter_mappings:
@@ -111,8 +120,7 @@ class MagneticFieldFactory(Loggable, object):
                 mapping = self.variable_to_parameter_mappings[variable_name]
                 mapped_variable = unity_mapper(variables[variable_name],
                                                a=mapping[0],
-                                               m=mapping[1],
-                                               b=mapping[2])
+                                               b=mapping[1])
 #                mapped_variable = carrier_mapper(variables[variable_name],
 #                                                 a=mapping[0],
 #                                                 m=mapping[1],

imagine/magnetic_fields/wmap3yr_magnetic_field/wmap3yr_magnetic_field_factory.py

@@ -31,7 +31,7 @@ class WMAP3yrMagneticFieldFactory(MagneticFieldFactory):
             'psi0': self._positive_interval(27.0, 5.0, n),  # psi0 astro-ph/0603450
             'psi1': self._positive_interval(0.9, 5.0, n),  # psi1 astro-ph/0603450
             'chi0': self._positive_interval(25, 5.0, n),  # xsi0 astro-ph/0603450
-            'random_rms': self._positive_interval(1.0, 2.0, n),
-            'random_rho': self._positive_interval(0.5, 1/6., n)
+            'random_rms': self._positive_interval(1.0, 1.0, n),
+            'random_rho': self._positive_interval(0.5, 0.166, n)
         }
         return defaults

imagine/observers/hammurapy/hammurapy.py

@@ -98,62 +98,6 @@ class Hammurapy(Observer):
                                     distribution_strategy='equal')
         return observable_dict
 
-    def _build_parameter_dict(self, parameter_dict, magnetic_field,
-                              local_ensemble_index):
-
-        parameter_dict.update(self.magnetic_field_model.parameter_dict)
-
-        parameter_dict.update(
-                {('./Interface/fe_grid', 'read'): '1',
-                 ('./Interface/fe_grid', 'filename'):
-                     os.path.join(self.input_directory, 'fe_grid.bin'),
-                 })
-        # access the magnetic-field's random-seed d2o directly, since we
-        # know that the distribution strategy is the same for the
-        # randam samples and the magnetic field itself
-        random_seed = magnetic_field.random_seed.data[local_ensemble_index]
-        parameter_dict.update(
-                {('./Galaxy/MagneticField/Random', 'seed'): random_seed})
-
-        for key, value in magnetic_field.parameters.iteritems():
-            large_key = magnetic_field.descriptor_lookup[key]
-            parameter_dict[large_key] = value
-
-        grid_space = magnetic_field.domain[1]
-        lx, ly, lz = np.array(grid_space.shape)*np.array(grid_space.distances)
-        nx, ny, nz = grid_space.shape
-
-        parameter_dict.update({('./Grid/Box/lx', 'value'): lx,
-                               ('./Grid/Box/ly', 'value'): ly,
-                               ('./Grid/Box/lz', 'value'): lz,
-                               ('./Grid/Box/nx', 'value'): nx,
-                               ('./Grid/Box/ny', 'value'): ny,
-                               ('./Grid/Box/nz', 'value'): nz})
-        parameter_dict.update(
-                {('./Grid/Integration/nside', 'value'): self.nside})
-
-    def _write_parameter_file(self, working_directory):
-        # load the default xml
-        try:
-            default_parameters_xml = os.path.join(self.input_directory,
-                                                  'default_parameters.xml')
-            tree = et.parse(default_parameters_xml)
-        except IOError:
-            import imagine
-            module_path = os.path.split(
-                            imagine.observers.hammurapy.__file__)[0]
-            default_parameters_xml = os.path.join(
-                                module_path, 'input/default_parameters.xml')
-            tree = et.parse(default_parameters_xml)
-
-        root = tree.getroot()
-        for key, value in parameter_dict.iteritems():
-            root.find(key[0]).set(key[1], str(value))
-
-        parameters_file_path = os.path.join(working_directory,
-                                            'parameters.xml')
-        tree.write(parameters_file_path)
-
     def _write_parameter_xml(self, magnetic_field, local_ensemble_index,
                              working_directory):
         # load the default xml
@@ -175,6 +119,7 @@ class Hammurapy(Observer):
         custom_parameters = [
                 ['./Grid/Integration/shell/auto/nside_min', 'value',
                  self.nside],
+                ['./Grid/Integration/nside_sim', 'value', self.nside],
                 ['./Interface/fe_grid', 'read', '1'],
                 ['./Interface/fe_grid', 'filename',
                  os.path.join(self.input_directory, 'fe_grid.bin')]

imagine/observers/hammurapy/input/default_parameters.xml

@@ -71,7 +71,7 @@
             </shell>
             <nside_sim value="16"/> <!-- output map resolution -->
             <!-- maximum radius in earth/Galactic centric frame -->
-            <ec_r_max value="30.0"/> <!-- kpc -->
+            <ec_r_max value="3.0"/> <!-- kpc -->
             <gc_r_max value="20.0"/> <!-- kpc -->
             <!-- maximum height in galactic centric frame -->
             <gc_z_max value="10.0"/> <!-- kpc -->
@@ -209,8 +209,7 @@
                 <!-- verification -->
                 <Verify>
                     <n0 value="0.01"/> <!-- pccm -->
-                    <r0 value="20.0"/> <!-- kpc -->
-                    <z0 value="0.1"/> <!-- kpc -->
+                    <r0 value="3.0"/> <!-- kpc -->
                 </Verify>
             </Regular>
             <!-- turbulent free electron -->
@@ -257,8 +256,7 @@
         <!-- verification -->
         <Verify>
             <alpha value="3.0"/>
-            <r0 value="20.0"/> <!-- kpc -->
-            <z0 value="1.0"/> <!-- kpc -->
+            <r0 value="3.0"/> <!-- kpc -->
             <je value="0.25"/> <!-- local CRE flux norm factor @ 10GeV -->
         </Verify>