Merge pull request #242 from LSSTDESC/roman_rubin

evevkovacs · web-flow · commit 87bf869f532b · 2024-12-31T10:02:40.000-07:00
Roman_Rubin Updates
diff --git a/batch_scripts/slurm_example_parallel.sh b/batch_scripts/slurm_example_parallel.sh
@@ -0,0 +1,12 @@
+#!/bin/bash
+#SBATCH -A m1727
+#SBATCH -C cpu
+#SBATCH -q regular
+#SBATCH -t 8:00:00
+#SBATCH --nodes=1
+#SBATCH --ntasks=8
+#SBATCH --cpus-per-task=32
+
+export OMP_NUM_THREADS=32
+
+./run_master.sh -p /global/cfs/projectdirs/lsst/groups/SRV/gcr-catalogs -c skysim5000_v1.2 -t tpcf_Wang2013_rSDSS_jack
diff --git a/batch_scripts/slurm_example_serial.sh b/batch_scripts/slurm_example_serial.sh
@@ -0,0 +1,13 @@
+#!/bin/bash
+#SBATCH -A m1727
+#SBATCH -C cpu
+#SBATCH -q regular
+#SBATCH -t 8:00:00
+#SBATCH --nodes=1
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=128
+
+export OMP_NUM_THREADS=32
+
+./run_master.sh -c skysim5000_v1.2 -t Nz_r_DEEP2_JAN_fig
+
diff --git a/batch_scripts/slurm_example_serial_DSigma.sh b/batch_scripts/slurm_example_serial_DSigma.sh
@@ -0,0 +1,12 @@
+#!/bin/bash
+#SBATCH -A m1727
+#SBATCH -C cpu
+#SBATCH -q regular
+#SBATCH -t 8:00:00
+#SBATCH --nodes=1
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=128
+
+export OMP_NUM_THREADS=32
+
+./run_master.sh -c skysim5000_v1.2_image -t delta_sigma_sdss_lowz
diff --git a/batch_scripts/slurm_example_serial_shear.sh b/batch_scripts/slurm_example_serial_shear.sh
@@ -0,0 +1,12 @@
+#!/bin/bash
+#SBATCH -A m1727
+#SBATCH -C cpu
+#SBATCH -q regular
+#SBATCH -t 8:00:00
+#SBATCH --nodes=1
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=128
+
+export OMP_NUM_THREADS=32
+
+./run_master.sh -c skysim5000_v1.2 -t shear
diff --git a/batch_scripts/slurm_example_serial_tpcf_color.sh b/batch_scripts/slurm_example_serial_tpcf_color.sh
@@ -0,0 +1,12 @@
+#!/bin/bash
+#SBATCH -A m1727
+#SBATCH -C cpu
+#SBATCH -q regular
+#SBATCH -t 8:00:00
+#SBATCH --nodes=1
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=128
+
+export OMP_NUM_THREADS=32
+
+./run_master.sh -c skysim5000_v1.2_image -t tpcf_Zehavi2011_color_fig
diff --git a/descqa/CheckColors.py b/descqa/CheckColors.py
@@ -59,7 +59,7 @@ class kernelCompare:
     def __init__(self,D1, D2):
         self._D1 = D1
         self._D2 = D2
-        self._XY = np.vstack((D1, D2))
+        self._XY = np.vstack(list(D1, D2))
         self._scale = self._computeScale(self._XY)
         self._n1 = len(D1)
         self._n2 = len(D2)
diff --git a/descqa/DeltaSigmaTest.py b/descqa/DeltaSigmaTest.py
@@ -180,7 +180,7 @@ def run_on_single_catalog(self, catalog_instance, catalog_name, output_dir):
             gt = gt/counts
 
             outfile = os.path.join(output_dir, 'DS_'+str(self.data)+'_'+str(i)+'.dat')
-            np.savetxt(outfile, np.vstack((rp.value, gt.value)).T)
+            np.savetxt(outfile, np.vstack(list(rp.value, gt.value)).T)
 
             
             if self.data == 'sdss_lowz':
diff --git a/descqa/EllipticityDistribution.py b/descqa/EllipticityDistribution.py
@@ -28,7 +28,7 @@ class EllipticityDistribution(BaseValidationTest):
             'band_Mag': ['V', 'r', 'g'],
             'zlo': 0.0,
             'zhi': 2.0,
-            'definition': 'e_squared',
+            'definition': 'e_distortion',
             'morphology': ('LRG', 'early', 'disk', 'late'),
             'filename_template': 'ellipticity/COSMOS/joachimi_et_al_2013/{}{}_{}.dat',
             'file-info': {
@@ -46,22 +46,27 @@ class EllipticityDistribution(BaseValidationTest):
                 'disk':{'B/T_min':0., 'B/T_max':0.2, 'mag_lo':24., 'Mag_hi':-21., 'Mag_lo':-17.},
                 'late':{'B/T_min':0.4, 'B/T_max':0.7, 'mag_lo':24., 'Mag_hi':-21., 'Mag_lo':-17.},
                 'irregular':{'B/T_min':0.0, 'B/T_max':1.0},
-                'ancillary_quantities':['bulge_to_total_ratio_i', 'bulge_to_total_ratio_stellar'],
+                'ancillary_quantities':['bulge_to_total_ratio_i', 'bulge_to_total_ratio_stellar',
+                                        'bulge_to_total_ratio'],
                 'ancillary_keys':['B/T'],
             },
         },
     }
     
     #define ellipticity functions
     @staticmethod
-    def e_default(e):
+    def e_shear(e):
         return e
 
     @staticmethod
-    def e_squared(a, b):
+    def e_distortion(a, b):
         q = b/a
         return  (1-q**2)/(1+q**2)
 
+    @staticmethod
+    def e_shear_to_distortion(e):
+        return 2*e/(1+e**2)
+
     #plotting constants
     lw2 = 2
     fsize = 16
@@ -86,6 +91,8 @@ def __init__(self, z='redshift_true', zlo=0., zhi=2., N_ebins=40, observation=''
         self.yfont_size = kwargs.get('yfont_size', 14)
         self.legend_size = kwargs.get('legend_size', 6)
         self.legend_title_size = kwargs.get('legend_title_size', 8)
+        self.catalog_ellipticity_definition = kwargs.get('ellipticity_definition', 'e_shear')
+        self.convert_to_distortion = kwargs.get('convert_to_distortion', False)
 
         possible_mag_fields = ('mag_{}_lsst',
                                'mag_{}_sdss',
@@ -103,16 +110,16 @@ def __init__(self, z='redshift_true', zlo=0., zhi=2., N_ebins=40, observation=''
         possible_native_luminosities = {'V':'otherLuminosities/totalLuminositiesStellar:V:rest',
                                        }
 
-        possible_ellipticity_definitions = {'e_default':{'possible_quantities':[['ellipticity', 'ellipticity_true']],
-                                                         'function':self.e_default,
-                                                         'xaxis_label': r'$e = (1-q)/(1+q)$',
-                                                         'file_label':'e',
-                                                        },
-                                            'e_squared':{'possible_quantities':[['size', 'size_true'], ['size_minor', 'size_minor_true']],
-                                                         'function':self.e_squared,
-                                                         'xaxis_label': r'$e = (1-q^2)/(1+q^2)$',
-                                                         'file_label':'e2',
-                                                        },
+        possible_ellipticity_definitions = {'e_shear':{'possible_quantities':[['ellipticity', 'ellipticity_true']],
+                                                       'function':self.e_shear,
+                                                       'xaxis_label': r'$e = (1-q)/(1+q)$',
+                                                       'file_label':'es',
+                                                      },
+                                            'e_distortion':{'possible_quantities':[['size', 'size_true'], ['size_minor', 'size_minor_true']],
+                                                            'function':self.e_distortion,
+                                                            'xaxis_label': r'$e = (1-q^2)/(1+q^2)$',
+                                                            'file_label':'ed',
+                                                           },
                                            }
         #binning
         self.N_ebins = N_ebins
@@ -150,10 +157,16 @@ def __init__(self, z='redshift_true', zlo=0., zhi=2., N_ebins=40, observation=''
         self.Mag_hi = dict(zip(self.morphology, [self.validation_data.get('cuts', {}).get(m, {}).get('Mag_hi', Mag_hi) for m in self.morphology]))
 
         #check for ellipticity definitions
-        self.possible_quantities = possible_ellipticity_definitions[self.validation_data.get('definition', 'e_default')]['possible_quantities']
-        self.ellipticity_function = possible_ellipticity_definitions[self.validation_data.get('definition', 'e_default')].get('function')
-        self.xaxis_label = possible_ellipticity_definitions[self.validation_data.get('definition', 'e_default')].get('xaxis_label')
-        self.file_label = possible_ellipticity_definitions[self.validation_data.get('definition', 'e_default')].get('file_label')
+        self.possible_quantities = possible_ellipticity_definitions[self.validation_data.get('definition', 'e_shear')]['possible_quantities']
+        self.ellipticity_function = possible_ellipticity_definitions[self.validation_data.get('definition', 'e_shear')].get('function')
+        self.xaxis_label = possible_ellipticity_definitions[self.validation_data.get('definition', 'e_shear')].get('xaxis_label')
+        self.file_label = possible_ellipticity_definitions[self.validation_data.get('definition', 'e_shear')].get('file_label')
+
+        #check for ellipticity conversions and overwrite previous definitions
+        if self.convert_to_distortion and self.catalog_ellipticity_definition == 'e_shear':
+            self.possible_quantities = possible_ellipticity_definitions[self.catalog_ellipticity_definition]['possible_quantities']
+            self.ellipticity_function = self.e_shear_to_distortion
+            print('Converting from e_shear to e_distortion')
 
         #check for native quantities
         self.native_luminosities = dict(zip([band for band in possible_native_luminosities if band in self.band_Mag],\
@@ -235,6 +248,7 @@ def run_on_single_catalog(self, catalog_instance, catalog_name, output_dir):
                 required_quantities.append(found_quantity)
         if not catalog_instance.has_quantities(required_quantities + self.filter_quantities):
             return TestResult(skipped=True, summary='Missing some required quantities: {}'.format(', '.join(required_quantities)))
+        print('Required quantities', required_quantities)
         ancillary_quantity = None
         if self.possible_ancillary_quantities is not None:
             ancillary_quantity = catalog_instance.first_available(*self.possible_ancillary_quantities)
@@ -262,7 +276,7 @@ def run_on_single_catalog(self, catalog_instance, catalog_name, output_dir):
                  fontsize=self.yfont_size) #setup a common axis label
 
         #initialize arrays for storing histogram sums
-        N_array = np.zeros((self.nrows, self.ncolumns, len(self.ebins)-1), dtype=np.int)
+        N_array = np.zeros((self.nrows, self.ncolumns, len(self.ebins)-1), dtype=int)
         sume_array = np.zeros((self.nrows, self.ncolumns, len(self.ebins)-1))
         sume2_array = np.zeros((self.nrows, self.ncolumns, len(self.ebins)-1))
         
@@ -477,7 +491,7 @@ def save_quantities(keyname, results, filename, comment=''):
             else:
                 fields = ('e_ave', keyname)
                 header = ', '.join(('Data columns are: <e>', keyname, ' '))
-            np.savetxt(filename, np.vstack((results[k] for k in fields)).T, fmt='%12.4e', header=header+comment)
+            np.savetxt(filename, np.vstack([results[k] for k in fields]).T, fmt='%12.4e', header=header+comment)
 
 
     def conclude_test(self, output_dir):
diff --git a/descqa/NumberDensityVersusRedshift.py b/descqa/NumberDensityVersusRedshift.py
@@ -106,14 +106,16 @@ def __init__(self, band='i', N_zbins=10, zlo=0., zhi=1.1,
         # pylint: disable=W0231
 
         #catalog quantities
-        self.truncate_cat_name = kwargs.get('truncate_cat_name', False)
+        self.truncate_cat_name = kwargs.get('truncate_cat_name', 0)
         self.replace_cat_name = kwargs.get('replace_cat_name', {})
         self.title_in_legend = kwargs.get('title_in_legend', False)
         self.legend_location = kwargs.get('legend_location', 'upper left')
         self.font_size = kwargs.get('font_size', 16)
         self.legend_size = kwargs.get('legend_size', 10)
         self.tick_size = kwargs.get('tick_size', 12)
         self.adjust_ylim = kwargs.get('adjust_ylim', 1.3)
+        self.include_reference = kwargs.get('include_reference', False)
+        self.insert_line_break = kwargs.get('insert_line_break', True)
         self.rest_frame = rest_frame
         if self.rest_frame:
             possible_mag_fields = ('Mag_true_{}_lsst_z0',
@@ -250,8 +252,11 @@ def run_on_single_catalog(self, catalog_instance, catalog_name, output_dir):
         filelabel = '_'.join((filtername, self.band))
 
         #setup plots
-        if self.truncate_cat_name:
-            catalog_name = re.split('_', catalog_name)[0]
+        if self.truncate_cat_name > 0:
+            possible_names = re.split('_', catalog_name)
+            catalog_name = possible_names[0]
+            for n in range(1, self.truncate_cat_name):
+                catalog_name = '_'.join((catalog_name, possible_names[n]))
         if self.replace_cat_name:
             for k, v in self.replace_cat_name.items():
                 catalog_name = re.sub(k, v, catalog_name)
@@ -261,7 +266,7 @@ def run_on_single_catalog(self, catalog_instance, catalog_name, output_dir):
         catalog_marker = next(self.markers)
 
         #initialize arrays for storing histogram sums
-        N_array = np.zeros((self.nrows, self.ncolumns, len(self.zbins)-1), dtype=np.int)
+        N_array = np.zeros((self.nrows, self.ncolumns, len(self.zbins)-1), dtype=int)
         sumz_array = np.zeros((self.nrows, self.ncolumns, len(self.zbins)-1))
 
         jackknife_data = {}
@@ -345,8 +350,11 @@ def run_on_single_catalog(self, catalog_instance, catalog_name, output_dir):
                 Nerrors = np.sqrt(np.diag(covariance))
 
                 #make subplot
-                catalog_label = ' '.join((catalog_name, cut_label.replace(self.band, filtername + ' ' + self.band)))
-                validation_label = ' '.join((self.validation_data.get('label', ''), cut_label))
+                line_break = '\n' if self.insert_line_break else ''
+                catalog_label = ' '.join((catalog_name, line_break,
+                                          cut_label.replace(self.band, filtername + ' ' + self.band)))
+                val_label = self.validation_data.get('label', '') if self.include_reference else ''
+                validation_label = ' '.join((val_label, cut_label)) if val_label else cut_label
                 key = cut_label.replace('$', '').replace('\\leq', '<=')
                 results[key] = {'meanz': meanz, 'total':total, 'N':N, 'N+-':Nerrors}
                 self.catalog_subplot(ax_this, meanz, N, Nerrors, catalog_color, catalog_marker, catalog_label)
@@ -403,7 +411,7 @@ def get_jackknife_errors(self, N_jack, jackknife_data, N):
         _, jack_labels, _ = k_means(n_clusters=N_jack, random_state=0, X=nn, n_init='auto')
 
         #make histograms for jackknife regions
-        Njack_array = np.zeros((N_jack, len(self.zbins)-1), dtype=np.int)
+        Njack_array = np.zeros((N_jack, len(self.zbins)-1), dtype=int)
         for nj in range(N_jack):
             Njack_array[nj] = np.histogram(jackknife_data[self.zlabel][jack_labels != nj], self.zbins)[0]
 
diff --git a/descqa/StellarMassFunction.py b/descqa/StellarMassFunction.py
@@ -165,7 +165,7 @@ def run_on_single_catalog(self, catalog_instance, catalog_name, output_dir):
             catalog_name = catalog_name.partition("_")[0]
         
         #initialize arrays for storing histogram sums
-        N_array = np.zeros((self.nrows, self.ncolumns, len(self.Mbins)-1), dtype=np.int)
+        N_array = np.zeros((self.nrows, self.ncolumns, len(self.Mbins)-1), dtype=int)
         sumM_array = np.zeros((self.nrows, self.ncolumns, len(self.Mbins)-1))
         sumM2_array = np.zeros((self.nrows, self.ncolumns, len(self.Mbins)-1))
 
@@ -320,7 +320,7 @@ def save_quantities(keyname, results, filename, comment=''):
             else:
                 fields = ('M'+keyname, keyname)
                 header = ', '.join(('Data columns are: <M>', keyname, ' '))
-            np.savetxt(filename, np.vstack((results[k] for k in fields)).T, fmt='%12.4e', header=header+comment)
+            np.savetxt(filename, np.vstack(list(results[k] for k in fields)).T, fmt='%12.4e', header=header+comment)
 
 
     def conclude_test(self, output_dir):
diff --git a/descqa/apparent_mag_func_test.py b/descqa/apparent_mag_func_test.py
@@ -43,7 +43,7 @@ def __init__(self, band='r', band_lim=(24.0, 27.5), fractional_tol=0.4, observat
         """
         # pylint: disable=super-init-not-called
 
-        self.truncate_cat_name = kwargs.get('truncate_cat_name', False)
+        self.truncate_cat_name = kwargs.get('truncate_cat_name', 0)
         self.title_in_legend = kwargs.get('title_in_legend', False)
         self.skip_label_detail = kwargs.get('skip_label_detail', False)
         self.font_size = kwargs.get('font_size', 16)
@@ -52,6 +52,7 @@ def __init__(self, band='r', band_lim=(24.0, 27.5), fractional_tol=0.4, observat
         self.print_title = kwargs.get('print_title', False)
         self.min_mag = kwargs.get('min_mag', 19.)
         self.replace_cat_name = kwargs.get('replace_cat_name', {})
+        self.exclude_sky_area = kwargs.get('exclude_sky_area', True)
         
         # catalog quantities needed
         possible_mag_fields = ('mag_{}_cModel',
@@ -206,14 +207,19 @@ def run_on_single_catalog(self, catalog_instance, catalog_name, output_dir):
         upper_ax, lower_ax = fig.add_axes(upper_rect), fig.add_axes(lower_rect)
 
         # plot on both this plot and any summary plots
-        if self.truncate_cat_name:
-            catalog_name = re.split('_', catalog_name)[0]
+        if self.truncate_cat_name > 0:
+            possible_names = re.split('_', catalog_name)
+            catalog_name = possible_names[0]
+            for n in range(1, self.truncate_cat_name):
+                catalog_name = '_'.join((catalog_name, possible_names[n]))
         if self.replace_cat_name:
             for k, v in self.replace_cat_name.items():      
                 catalog_name = re.sub(k, v, catalog_name)
-                
-        upper_ax.plot(mag_bins, sampled_N, '-', label=catalog_name + sky_area_label)
-        self.summary_upper_ax.plot(mag_bins, sampled_N, '-', label=catalog_name + sky_area_label)
+
+        cat_label = catalog_name if self.exclude_sky_area else catalog_name + sky_area_label
+                            
+        upper_ax.plot(mag_bins, sampled_N, '-', label=cat_label)
+        self.summary_upper_ax.plot(mag_bins, sampled_N, '-', label=cat_label)
 
         # plot validation data
         n = self.validation_data['n(<mag)']
diff --git a/descqa/clf_redmapper.py b/descqa/clf_redmapper.py
@@ -39,11 +39,11 @@ def count_galaxies_p_cen(cenmag, lumbins, p_cen):
     dlum = lumbins[1] - lumbins[0]
     minlum = lumbins[0] - dlum / 2.0
     chto_countArray = np.zeros([len(cenmag), nlum])
-    mybin = np.floor((cenmag[:, :] - minlum) / dlum).astype(np.int)
+    mybin = np.floor((cenmag[:, :] - minlum) / dlum).astype(int)
     p_cen = p_cen.reshape(-1, 1)
     ncen = np.zeros(p_cen.shape)
     ncen = np.hstack(((np.ones(p_cen.shape[0])).reshape(-1, 1), ncen[:, :-1])).astype(
-        np.int
+        int
     )
     weight = p_cen
 
diff --git a/descqa/configs/ApparentMagFuncTest_HSCr_fig.yaml b/descqa/configs/ApparentMagFuncTest_HSCr_fig.yaml
@@ -5,10 +5,10 @@ observation: 'HSC'
 included_by_default: true
 print_title: false
 x_lower_limit: 19
-truncate_cat_name: true
+truncate_cat_name: 2
 font_size: 18
 legend_size: 12
 skip_label_detail: true
-replace_cat_name: {'dc2':'DC2'}
+replace_cat_name: {'roman_rubin':'OpenUniverse2024'}
 
 description: 'Plot N(<mag) distributions for selected magnitude bounds in specified band and compare with extrpolated fits to HSC deep fields data.'
diff --git a/descqa/configs/Nz_r_Coil2004_maglim_fig.yaml b/descqa/configs/Nz_r_Coil2004_maglim_fig.yaml
@@ -7,7 +7,8 @@ observation: 'Coil2004_maglim'
 jackknife: True
 N_jack: 30
 use_diagonal_only: True
-truncate_cat_name: True
+truncate_cat_name: 2
+replace_cat_name: {'roman_rubin':'OpenUniverse2024'}
 legend_size: 12
 font_size: 18
 
diff --git a/descqa/configs/ellipticity_shear_COSMOS_fig.yaml b/descqa/configs/ellipticity_shear_COSMOS_fig.yaml
@@ -0,0 +1,23 @@
+subclass_name: EllipticityDistribution.EllipticityDistribution
+zlo: 0.
+zhi: 2.
+N_ebins: 40
+observation: 'COSMOS_2013'
+normed: True
+convert_to_distortion: True
+validation_percentile_points:
+  - 10
+  - 50
+  - 90
+validation_percentile_ranges:
+  - [0, 0.4]
+  - [0.3, 0.7]
+  - [0.6, 1]
+truncate_cat_name: true
+title_in_legend: true
+yfont_size: 14
+xfont_size: 12
+legend_size: 10
+legend_title_size: 10
+
+description: 'Plot ellipticity distributions and compare with distributions from Joachimi et al 2013 COSMOS data'
diff --git a/descqa/shear_test.py b/descqa/shear_test.py
diff --git a/descqa/stats.py b/descqa/stats.py
