mimical 0.0.9__tar.gz → 0.1.1__tar.gz

{mimical-0.0.9 → mimical-0.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mimical
-Version: 0.0.9
+Version: 0.1.1
 Summary: Intesity modelling of multiply-imaged objects
 Author: Struan Stevenson
 Author-email: struan.stevenson@ed.ac.uk
@@ -17,7 +17,7 @@ Dynamic: description-content-type
 Dynamic: requires-dist
 Dynamic: summary
 
-# Mimical (Modelling the Intensity of Multiply-Imaged CelestiAl Light)
+# Mimical (Modelling the Intensity of Multiply-Imaged Celestial Ancient Light)
 
 
 #### Mimical is an intensity modelling code for multiply-imaged objects, performing simultaenous Bayseian inference of model parameters via the nested sampling algorithm. Mimical supports any astropy model, and supports user defined parameter polynomial depenency with image wavelength.

{mimical-0.0.9 → mimical-0.1.1}/README.md

@@ -1,4 +1,4 @@
-# Mimical (Modelling the Intensity of Multiply-Imaged CelestiAl Light)
+# Mimical (Modelling the Intensity of Multiply-Imaged Celestial Ancient Light)
 
 
 #### Mimical is an intensity modelling code for multiply-imaged objects, performing simultaenous Bayseian inference of model parameters via the nested sampling algorithm. Mimical supports any astropy model, and supports user defined parameter polynomial depenency with image wavelength.

{mimical-0.0.9 → mimical-0.1.1}/mimical/fitting/fitter.py

@@ -161,10 +161,11 @@ class mimical(object):
             self.success = True
             self.samples = pd.read_csv(dir_path+'/mimical/posteriors' + f'/{self.id}.txt', delimiter=' ').to_numpy()
             fit_dic = dict(zip((np.array((list(self.fitter_prior.keys)))+"_50").tolist(), np.median(self.samples, axis=0).tolist()))
-            print("Finished.")
+            print(f"Loading existing posterior at " + dir_path + '/mimical/posteriors' + f'/{self.id}.txt')
             print(" ")
             return fit_dic
 
+
         # Run sampler
         t0 = time.time()
         #sampler = Sampler(self.fitter_prior, self.lnlike, n_live=400, filepath= dir_path+'/bogout'+f'/{self.id}.hdf5', resume=True, pool=self.pool)
@@ -184,7 +185,7 @@ class mimical(object):
 
             # Plot and save the corner plot
             corner.corner(points, weights=np.exp(log_w), bins=20, labels=np.array(self.fitter_prior.keys), color='purple', plot_datapoints=False, range=np.repeat(0.999, len(self.fitter_prior.keys)))
-            plt.savefig(dir_path+'/mimical/plots' + f'/corner_{self.id}.pdf', bbox_inches='tight')
+            plt.savefig(dir_path+'/mimical/plots' + f'/{self.id}_corner.pdf', bbox_inches='tight')
 
             # Sample an appropriately weighted posterior for representative samples.
             n_post = 10000
@@ -196,18 +197,23 @@ class mimical(object):
             # Return the median-parameter model
             fit_dic = dict(zip((np.array((list(self.fitter_prior.keys)))+"_50").tolist(), np.median(self.samples, axis=0).tolist()))
 
-            print("Finished.")
+            print("Sampling finished successfully.")
             print(" ")
 
             return fit_dic
     
 
-    def plot_model(self):
+    def plot_model(self, type='median'):
         if self.success != True:
-            print(f'Failed sampling, cannot plot model for {self.id}.')
+            print(f'Sampling failed, cannot plot model for {self.id}.')
         else:
-            # Plot and save the median-parameter fit
-            Plotter().plot_median(self.images, self.wavs, self.convolved_models, self.samples, list(self.fitter_prior.keys), self.prior_handler)
-            plt.savefig(dir_path+'/mimical/plots' + f'/{self.id}_best_model.pdf', bbox_inches='tight')
+            if type=='median':
+                # Plot and save the median-parameter fit
+                Plotter().plot_median(self.images, self.wavs, self.convolved_models, self.samples, list(self.fitter_prior.keys), self.prior_handler, self.filter_names)
+                plt.savefig(dir_path+'/mimical/plots' + f'/{self.id}_median_model.pdf', bbox_inches='tight')
+            elif type=='median-param':
+                # Plot and save the median-parameter fit
+                Plotter().plot_median_param(self.images, self.wavs, self.convolved_models, self.samples, list(self.fitter_prior.keys), self.prior_handler, self.filter_names)
+                plt.savefig(dir_path+'/mimical/plots' + f'/{self.id}_median_param_model.pdf', bbox_inches='tight')
 
    

mimical-0.1.1/mimical/plotting/plotting.py

@@ -0,0 +1,165 @@
+import matplotlib.pyplot as plt
+import numpy as np
+from astropy.convolution.utils import discretize_model
+from tqdm import tqdm
+from matplotlib import ticker
+
+class Plotter(object):   
+
+    def plot_median_param(self, images, wavs, convolved_models, samples, fitter_keys, prior_handler, filter_names):
+
+        fig = plt.figure()
+        gs = fig.add_gridspec(nrows=4, ncols=images.shape[0]+1, width_ratios=np.append(np.ones(images.shape[0]), 0.25))
+
+        
+        # Get median Nautilus parameters and transalte into median model parameters.
+        param_dict = dict(zip(fitter_keys, np.median(samples, axis=0)))
+        pars = prior_handler.revert(param_dict, wavs)
+
+
+        models = np.zeros_like(images)
+        for i in range(len(wavs)):
+            convolved_models[i].parameters = pars[i]
+            model = discretize_model(model=convolved_models[i], 
+                                    x_range=[0,images[i].shape[1]], 
+                                    y_range=[0,images[i].shape[0]], 
+                                    mode='center')
+            models[i]=model
+
+        
+        residuals = images - models
+
+        vmins = [-np.percentile(images.flatten(), q=95), -np.percentile(images.flatten(), q=95), -np.percentile(images.flatten(), q=95), min(np.percentile(residuals.flatten(), q=5), -np.percentile(residuals.flatten(), q=95))]
+        vmaxs = [np.percentile(images.flatten(), q=95), np.percentile(images.flatten(), q=95), np.percentile(images.flatten(), q=95), max(-np.percentile(residuals.flatten(), q=5), np.percentile(residuals.flatten(), q=95))]
+        cmaps = ['binary', 'binary', 'RdGy']
+
+        ax = fig.add_subplot(gs[0, 0])
+        ax.set_axis_off()
+        im1 = ax.pcolormesh(np.zeros_like(images[0]), vmax=vmaxs[0], vmin=vmins[0], cmap='RdGy')
+        cbarax1 = fig.add_subplot(gs[:3, -1])
+        cbarax1.set_yticks([])
+        cbarax1.set_xticks([])
+        cbar1 = plt.colorbar(im1, cax=cbarax1, fraction=1)
+        tick_locator = ticker.MaxNLocator(nbins=5)
+        cbar1.locator = tick_locator
+        cbar1.update_ticks()
+
+        im2 = ax.pcolormesh(np.zeros_like(images[0]), vmax=vmaxs[-1], vmin=vmins[-1], cmap='RdGy')
+        cbarax2 = fig.add_subplot(gs[3, -1])
+        cbarax2.set_yticks([])
+        cbarax2.set_xticks([])
+        cbar2 = plt.colorbar(im2, cax=cbarax2, fraction=1)
+        tick_locator = ticker.MaxNLocator(nbins=3)
+        cbar2.locator = tick_locator
+        cbar2.update_ticks()
+
+        for i in range(len(wavs)):
+
+            plotims = [images[i], models[i], residuals[i], residuals[i]]
+
+            for j in range(4):
+
+                ax = fig.add_subplot(gs[j, i])
+                im = ax.pcolormesh(plotims[j], vmax=vmaxs[j], vmin=vmins[j], cmap='RdGy')
+                ax.set_yticks([])
+                ax.set_xticks([])
+
+                if j==0:
+                    ax.set_title(filter_names[i].upper())
+
+                if i==0:
+                    if j==0:
+                        ax.set_ylabel('Data')
+                    if j==1:
+                        ax.set_ylabel('Best\nModel')
+                    if j==2:
+                        ax.set_ylabel('Residual')
+                    if j==3:
+                        ax.set_ylabel('Residual\nZoom')
+
+        
+        plt.subplots_adjust(hspace=0.1, wspace=0.1)
+        fig.set_size_inches(images.shape[0],4, forward=True)
+
+
+
+
+
+    def plot_median(self, images, wavs, convolved_models, samples, fitter_keys, prior_handler, filter_names):
+
+        fig = plt.figure()
+        gs = fig.add_gridspec(nrows=4, ncols=images.shape[0]+1, width_ratios=np.append(np.ones(images.shape[0]), 0.25))
+        
+        models = np.zeros((samples.shape[0], *images.shape))
+
+        print("Computing median model image...")
+        for j in tqdm(range(samples.shape[0])):
+            # Get median Nautilus parameters and transalte into median model parameters.
+            param_dict = dict(zip(fitter_keys, samples[j]))
+            pars = prior_handler.revert(param_dict, wavs)
+
+            for k in range(len(wavs)):
+                convolved_models[k].parameters = pars[k]
+                model = discretize_model(model=convolved_models[k], 
+                                        x_range=[0,images[k].shape[1]], 
+                                        y_range=[0,images[k].shape[0]], 
+                                        mode='center')
+                models[j,k] = model
+
+
+        models = np.median(models, axis=0)
+        residuals = images - models
+
+
+        vmins = [-np.percentile(images.flatten(), q=95), -np.percentile(images.flatten(), q=95), -np.percentile(images.flatten(), q=95), min(np.percentile(residuals.flatten(), q=5), -np.percentile(residuals.flatten(), q=95))]
+        vmaxs = [np.percentile(images.flatten(), q=95), np.percentile(images.flatten(), q=95), np.percentile(images.flatten(), q=95), max(-np.percentile(residuals.flatten(), q=5), np.percentile(residuals.flatten(), q=95))]
+        cmaps = ['binary', 'binary', 'RdGy']
+
+        ax = fig.add_subplot(gs[0, 0])
+        ax.set_axis_off()
+        im1 = ax.pcolormesh(np.zeros_like(images[0]), vmax=vmaxs[0], vmin=vmins[0], cmap='RdGy')
+        cbarax1 = fig.add_subplot(gs[:3, -1])
+        cbarax1.set_yticks([])
+        cbarax1.set_xticks([])
+        cbar1 = plt.colorbar(im1, cax=cbarax1, fraction=1)
+        tick_locator = ticker.MaxNLocator(nbins=5)
+        cbar1.locator = tick_locator
+        cbar1.update_ticks()
+
+        im2 = ax.pcolormesh(np.zeros_like(images[0]), vmax=vmaxs[-1], vmin=vmins[-1], cmap='RdGy')
+        cbarax2 = fig.add_subplot(gs[3, -1])
+        cbarax2.set_yticks([])
+        cbarax2.set_xticks([])
+        cbar2 = plt.colorbar(im2, cax=cbarax2, fraction=1)
+        tick_locator = ticker.MaxNLocator(nbins=3)
+        cbar2.locator = tick_locator
+        cbar2.update_ticks()
+
+        for i in range(len(wavs)):
+
+            plotims = [images[i], models[i], residuals[i], residuals[i]]
+
+            for j in range(4):
+
+                ax = fig.add_subplot(gs[j, i])
+                im = ax.pcolormesh(plotims[j], vmax=vmaxs[j], vmin=vmins[j], cmap='RdGy')
+                ax.set_yticks([])
+                ax.set_xticks([])
+
+                if j==0:
+                    ax.set_title(filter_names[i].upper())
+
+                if i==0:
+                    if j==0:
+                        ax.set_ylabel('Data')
+                    if j==1:
+                        ax.set_ylabel('Median\nModel')
+                    if j==2:
+                        ax.set_ylabel('Residual')
+                    if j==3:
+                        ax.set_ylabel('Residual\nZoom')
+
+        
+        plt.subplots_adjust(hspace=0.1, wspace=0.1)
+        fig.set_size_inches(images.shape[0],4, forward=True)
+

{mimical-0.0.9 → mimical-0.1.1}/mimical.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mimical
-Version: 0.0.9
+Version: 0.1.1
 Summary: Intesity modelling of multiply-imaged objects
 Author: Struan Stevenson
 Author-email: struan.stevenson@ed.ac.uk
@@ -17,7 +17,7 @@ Dynamic: description-content-type
 Dynamic: requires-dist
 Dynamic: summary
 
-# Mimical (Modelling the Intensity of Multiply-Imaged CelestiAl Light)
+# Mimical (Modelling the Intensity of Multiply-Imaged Celestial Ancient Light)
 
 
 #### Mimical is an intensity modelling code for multiply-imaged objects, performing simultaenous Bayseian inference of model parameters via the nested sampling algorithm. Mimical supports any astropy model, and supports user defined parameter polynomial depenency with image wavelength.

{mimical-0.0.9 → mimical-0.1.1}/setup.py

@@ -8,7 +8,7 @@ long_description = (this_directory / "README.md").read_text()
 setup(
     name='mimical',
 
-    version='0.0.9',
+    version='0.1.1',
 
     description='Intesity modelling of multiply-imaged objects',
 

mimical-0.0.9/mimical/plotting/plotting.py

@@ -1,87 +0,0 @@
-import matplotlib.pyplot as plt
-import numpy as np
-from astropy.convolution.utils import discretize_model
-from tqdm import tqdm
-
-class Plotter(object):   
-
-    def plot_best(self, images, wavs, convolved_models, samples, fitter_keys, prior_handler):
-
-        fig,axes=plt.subplots(3, images.shape[0], figsize=(images.shape[0],3))
-        
-        # Get median Nautilus parameters and transalte into median model parameters.
-        param_dict = dict(zip(fitter_keys, np.median(samples, axis=0)))
-        pars = prior_handler.revert(param_dict, wavs)
-
-        for i in range(len(wavs)):
-            convolved_models[i].parameters = pars[i]
-            model = discretize_model(model=convolved_models[i], 
-                                    x_range=[0,images[i].shape[1]], 
-                                    y_range=[0,images[i].shape[0]], 
-                                    mode='center')
-            
-
-            v = np.percentile(images[-1], 99.9)
-
-            axes[0,i].imshow(images[i], vmax=v, vmin=-v)
-            axes[0,i].set_axis_off()
-
-            axes[1,i].imshow(model, vmax=v, vmin=-v)
-            axes[1,i].set_axis_off()
-
-            axes[2,i].imshow(images[i]-model, vmax=v, vmin=-v)
-            axes[2,i].set_axis_off()
-
-
-    def plot_median(self, images, wavs, convolved_models, samples, fitter_keys, prior_handler):
-
-        fig,axes=plt.subplots(3, images.shape[0], figsize=(images.shape[0],3))
-        
-
-        models = np.zeros((samples.shape[0], *images.shape))
-
-        print("Computing median model image...")
-        for j in tqdm(range(samples.shape[0])):
-            # Get median Nautilus parameters and transalte into median model parameters.
-            param_dict = dict(zip(fitter_keys, samples[j]))
-            pars = prior_handler.revert(param_dict, wavs)
-
-            for k in range(len(wavs)):
-                convolved_models[k].parameters = pars[k]
-                model = discretize_model(model=convolved_models[k], 
-                                        x_range=[0,images[k].shape[1]], 
-                                        y_range=[0,images[k].shape[0]], 
-                                        mode='center')
-                models[j,k] = model
-
-
-        median_models = np.median(models, axis=0)
-
-
-        if len(wavs)==1:
-            for i in range(len(wavs)):
-                v = np.percentile(images[-1], 99.9)
-
-                axes[0].imshow(images[i], vmax=v, vmin=-v)
-                axes[0].set_axis_off()
-
-                axes[1].imshow(median_models[i], vmax=v, vmin=-v)
-                axes[1].set_axis_off()
-
-                axes[2].imshow(images[i]-median_models[i], vmax=v, vmin=-v)
-                axes[2].set_axis_off()
-
-        else:
-            for i in range(len(wavs)):
-
-                v = np.percentile(images[-1], 99.9)
-
-                axes[0,i].imshow(images[i], vmax=v, vmin=-v)
-                axes[0,i].set_axis_off()
-
-                axes[1,i].imshow(median_models[i], vmax=v, vmin=-v)
-                axes[1,i].set_axis_off()
-
-                axes[2,i].imshow(images[i]-median_models[i], vmax=v, vmin=-v)
-                axes[2,i].set_axis_off()
-