adding TXGammaTRandoms stage

examples/laptop_pipeline.yml

@@ -18,6 +18,8 @@ stages:
       threads_per_process: 2
     - name: TXGammaTBrightStars
       threads_per_process: 2
+    - name: TXGammaTRandoms
+      threads_per_process: 2
     - name: TXGammaTDimStars
       threads_per_process: 2
     - name: TXRoweStatistics

txpipe/random_cats.py

@@ -137,6 +137,8 @@ def run(self):
                 ### Interpolate those random values to a redshift value given by the cdf
                 # z_photo_rand = np.interp(cdf_rand_val,z_cdf_norm,z_photo_arr)
                 z_interp_func = scipy.interpolate.interp1d(z_cdf_norm,z_photo_arr)
+                # Sometimes we don't quite go down to z - deal with that
+                cdf_rand_val = cdf_rand_val.clip(z_cdf_norm.min(), z_cdf_norm.max())
                 z_photo_rand = z_interp_func(cdf_rand_val)
 
                 # Save output

txpipe/twopoint.py

@@ -1528,6 +1528,172 @@ def write_output_sacc(self, data, meta, results):
 
         # Also make a plot of the data
 
+class TXGammaTRandoms(TXTwoPoint):
+    """
+    This subclass of the standard TXTwoPoint uses the centers
+    of stars as "lenses", as a systematics test.
+    """
+    name = "TXGammaTRandoms"
+    inputs = [
+        ('shear_catalog', ShearCatalog),
+        ('shear_tomography_catalog', TomographyCatalog),
+        ('shear_photoz_stack', HDFFile),
+        ('lens_tomography_catalog', TomographyCatalog),
+        ('lens_photoz_stack', HDFFile),
+        ('random_cats', RandomsCatalog),
+        ('star_catalog', HDFFile),
+        ('patch_centers', TextFile),
+    ]
+    outputs = [
+        ('gammat_randoms', SACCFile),
+        ('gammat_randoms_plot', PNGFile),
+    ]
+    # Add values to the config file that are not previously defined
+    config_options = {
+        'calcs':[0,1,2],
+        'min_sep':2.5,
+        'max_sep':100,
+        'nbins':20,
+        'bin_slop':0.1,
+        'sep_units':'arcmin',
+        'flip_g2':True,
+        'cores_per_task':20,
+        'verbose':1,
+        'reduce_randoms_size':1.0,
+        'var_methods': 'jackknife',
+        'npatch': 5,
+        'shear_catalog_type': 'metacal',
+        }
+
+    def run(self):
+        # Before running the parent class we add source_bins and lens_bins
+        # options that it is expecting, both set to -1 to indicate that we
+        # will choose them automatically (below).
+        import matplotlib
+        matplotlib.use('agg')
+        self.config['source_bins'] = [-1]
+        self.config['lens_bins'] = [-1]
+        super().run()
+
+    def read_nbin(self, data):
+        # We use only a single source and lens bin in this case -
+        # the source is the complete 2D field and the lens is the
+        # field centers
+        data['source_list'] = [0]
+        data['lens_list'] = [0]
+
+    def load_random_catalog(self, data):
+        # override the parent method
+        # so that we don't load the randoms here,
+        # because if we subtract randoms from randoms
+        # we get nothing.
+        pass
+
+    def load_lens_catalog(self, data):
+        # We load the randoms to use as lenses
+        f = self.open_input('random_cats')
+        group = f['randoms']
+        data['lens_ra'] = group['ra'][:]
+        data['lens_dec'] = group['dec'][:]
+        f.close()
+
+        npoint = data['lens_ra'].size
+        data['lens_bin'] = np.zeros(npoint)
+
+    def load_tomography(self, data):
+        # We run the parent class tomography selection but then
+        # overrided it to squash all of the bins  0 .. nbin -1
+        # down to the zero bin.  This means that any selected
+        # objects (from any tomographic bin) are now in the same
+        # bin, and unselected objects still have bin -1
+        super().load_tomography(data)
+        data['source_bin'][:] = data['source_bin'].clip(-1,0)
+
+    def select_calculations(self, data):
+        # We only want a single calculation, the gamma_T around
+        # the field centers
+        return [(0,0,SHEAR_POS)]
+
+    def write_output(self, data, meta, results):
+        # we write output both to file for later and to
+        # a plot
+        self.write_output_sacc(data, meta, results)
+        self.write_output_plot(results)
+
+    def write_output_plot(self, results):
+        import matplotlib.pyplot as plt
+        d = results[0]
+        dvalue = d.object.xi
+        derror = np.sqrt(d.object.varxi)
+        dtheta = np.exp(d.object.meanlogr)
+
+        fig = self.open_output('gammat_randoms_plot', wrapper=True)
+
+        # compute the mean and the chi^2/dof
+        flat1 = 0
+        z = (dvalue - flat1) / derror
+        chi2 = np.sum(z ** 2)
+        chi2dof = chi2 / (len(dtheta) - 1)
+        print('error,',derror)
+
+        plt.errorbar(dtheta,  dtheta*dvalue, dtheta*derror, fmt='ro', capsize=3,label='$\chi^2/dof = $'+str(chi2dof))
+        plt.legend(loc='best')
+        plt.xscale('log')
+
+        plt.xlabel(r"$\theta$ / arcmin")
+        plt.ylabel(r"$\theta \cdot \gamma_t(\theta)$")
+        plt.title("Randoms Tangential Shear")
+
+        print('type',type(fig))
+        fig.close()
+
+    def write_output_sacc(self, data, meta, results):
+        # We write out the results slightly differently here
+        # beause they go to a different file and have different
+        # tracers and tags.
+        import sacc
+        dt = "galaxyRandoms_shearDensity_xi_t"
+
+        S = sacc.Sacc()
+
+        f = self.open_input('shear_photoz_stack')
+        z = f['n_of_z/source2d/z'][:]
+        Nz = f[f'n_of_z/source2d/bin_0'][:]
+        f.close()
+
+        # Add the data points that we have one by one, recording which
+        # tracer they each require
+        S.add_tracer('misc', 'randoms')
+        S.add_tracer('NZ', 'source2d', z, Nz)
+
+        d = results[0]
+        assert len(results)==1
+        dvalue = d.object.xi
+        derror = np.sqrt(d.object.varxi)
+        dtheta = np.exp(d.object.meanlogr)
+        dnpair = d.object.npairs
+        dweight = d.object.weight
+
+
+        # Each of our Measurement objects contains various theta values,
+        # and we loop through and add them all
+        n = len(dvalue)
+        for i in range(n):
+            S.add_data_point(dt, ('source2d', 'randoms'), dvalue[i],
+                theta=dtheta[i], error=derror[i], npair=dnpair[i], weight=dweight[i])
+
+        self.write_metadata(S, meta)
+
+        print(S)
+        # Our data points may currently be in any order depending on which processes
+        # ran which calculations.  Re-order them.
+        S.to_canonical_order()
+
+        # Finally, save the output to Sacc file
+        S.save_fits(self.get_output('gammat_randoms'), overwrite=True)
+
+        # Also make a plot of the data
+
 class TXJackknifeCenters(PipelineStage):
     """
     This is the pipeline stage that is run to generate the patch centers for