mimical 0.1.0__py3-none-any.whl → 0.1.2__py3-none-any.whl

mimical/fitting/fitter.py

@@ -14,11 +14,15 @@ from ..plotting import Plotter
 
 from ..utils import filter_set
 
+from tqdm import tqdm
+
+
 dir_path = os.getcwd()
 if not os.path.isdir(dir_path + "/mimical"):
     os.system('mkdir ' + dir_path + "/mimical")
     os.system('mkdir ' + dir_path + "/mimical/plots")
     os.system('mkdir ' + dir_path + "/mimical/posteriors")
+    os.system('mkdir ' + dir_path + "/mimical/cats")
 
 
 
@@ -162,6 +166,7 @@ class mimical(object):
             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(f"Loading existing posterior at " + dir_path + '/mimical/posteriors' + f'/{self.id}.txt')
+            self.save_cat()
             print(" ")
             return fit_dic
 
@@ -185,7 +190,7 @@ 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
@@ -200,15 +205,48 @@ class mimical(object):
             print("Sampling finished successfully.")
             print(" ")
 
+            self.save_cat()
+
             return fit_dic
+        
+    
+    def save_cat(self):
+
+        user_samples = np.zeros((self.samples.shape[0], len(self.wavs), len(self.user_prior.keys())))
+        # Get median Nautilus parameters and transalte into median model parameters.
+        for j in tqdm(range(self.samples.shape[0])):
+            # Get median Nautilus parameters and transalte into median model parameters.
+            param_dict = dict(zip(list(self.fitter_prior.keys), self.samples[j]))
+            pars = self.prior_handler.revert(param_dict, self.wavs)
+            user_samples[j] = pars
+
+        quantiles = np.percentile(user_samples, q=(16, 50, 84), axis=0)
+
+        dic = {}
+        for j in range(len(self.filter_names)):
+            for i in range(len(self.user_prior.keys())):
+                key = list(self.user_prior.keys())[i]
+                dic[key + "_" + self.filter_names[j] + "_16"] = [quantiles[0, j, i]]
+                dic[key + "_" + self.filter_names[j] + "_50"] = [quantiles[1, j, i]]
+                dic[key + "_" + self.filter_names[j] + "_84"] = [quantiles[2, j, i]]
+
+        df = pd.DataFrame(dic)
+        df.to_csv(dir_path+'/mimical/cats' + f'/{self.id}.csv', index=False)
+
+
     
 
-    def plot_model(self):
+    def plot_model(self, type='median'):
         if self.success != True:
             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/plotting/plotting.py

@@ -2,42 +2,94 @@ 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_best(self, images, wavs, convolved_models, samples, fitter_keys, prior_handler):
+    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))
 
-        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)
 
+
+        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
 
-            v = np.percentile(images[-1], 99.9)
+        
+        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()
 
-            axes[0,i].imshow(images[i], vmax=v, vmin=-v)
-            axes[0,i].set_axis_off()
+        for i in range(len(wavs)):
 
-            axes[1,i].imshow(model, vmax=v, vmin=-v)
-            axes[1,i].set_axis_off()
+            plotims = [images[i], models[i], residuals[i], residuals[i]]
 
-            axes[2,i].imshow(images[i]-model, vmax=v, vmin=-v)
-            axes[2,i].set_axis_off()
+            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([])
 
-    def plot_median(self, images, wavs, convolved_models, samples, fitter_keys, prior_handler):
+                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')
 
-        fig,axes=plt.subplots(3, images.shape[0], figsize=(images.shape[0],3))
         
+        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...")
@@ -55,33 +107,59 @@ class Plotter(object):
                 models[j,k] = model
 
 
-        median_models = np.median(models, axis=0)
+        models = np.median(models, axis=0)
+        residuals = images - models
 
 
-        if len(wavs)==1:
-            for i in range(len(wavs)):
-                v = np.percentile(images[-1], 99.9)
+        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']
 
-                axes[0].imshow(images[i], vmax=v, vmin=-v)
-                axes[0].set_axis_off()
+        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()
 
-                axes[1].imshow(median_models[i], vmax=v, vmin=-v)
-                axes[1].set_axis_off()
+        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()
 
-                axes[2].imshow(images[i]-median_models[i], vmax=v, vmin=-v)
-                axes[2].set_axis_off()
+        for i in range(len(wavs)):
+
+            plotims = [images[i], models[i], residuals[i], residuals[i]]
 
-        else:
-            for i in range(len(wavs)):
+            for j in range(4):
 
-                v = np.percentile(images[-1], 99.9)
+                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([])
 
-                axes[0,i].imshow(images[i], vmax=v, vmin=-v)
-                axes[0,i].set_axis_off()
+                if j==0:
+                    ax.set_title(filter_names[i].upper())
 
-                axes[1,i].imshow(median_models[i], vmax=v, vmin=-v)
-                axes[1,i].set_axis_off()
+                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')
 
-                axes[2,i].imshow(images[i]-median_models[i], vmax=v, vmin=-v)
-                axes[2,i].set_axis_off()
+        
+        plt.subplots_adjust(hspace=0.1, wspace=0.1)
+        fig.set_size_inches(images.shape[0],4, forward=True)
 

{mimical-0.1.0.dist-info → mimical-0.1.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mimical
-Version: 0.1.0
+Version: 0.1.2
 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-0.1.0.dist-info → mimical-0.1.2.dist-info}/RECORD

@@ -1,12 +1,12 @@
 mimical/__init__.py,sha256=cBuyDtPwn6KcIkjlT7oct36jigvYDJmbZNmnt1I1QJU,75
 mimical/fitting/__init__.py,sha256=xcnLoeBDtt4Le5NhD6GhJe2ZRPNSsEySRHFYNuJyNEQ,69
-mimical/fitting/fitter.py,sha256=jFFTRj2nsX1pchQdB9hxjxjvMNJyyF3qrpwOJTNakXM,8722
+mimical/fitting/fitter.py,sha256=BjPT3wgGJ_KO4iyB9n0t4cqn0jfpU9d4IT0Gc1COoJc,10489
 mimical/fitting/prior_handler.py,sha256=yXvxbohS6f94CMRyeIViFc83hRYAj82IZNA5mzhMSRw,4193
 mimical/plotting/__init__.py,sha256=I1ZpQA48g-YPkqwrDGgTrqaTxDUgR8n0mbBX0MdbZtU,30
-mimical/plotting/plotting.py,sha256=RW6PgrX3UbafXmUnthV0mttKRjeUnS03eeX1c6fgZHU,3131
+mimical/plotting/plotting.py,sha256=y6uNeUh3Ifp8fapTPyN2eKT3OfnRhfNCUYq3ZN6lei4,6708
 mimical/utils/__init__.py,sha256=yolMgYFpvXoHuyV-ijGo26SQ0_niw0gz__iAFgdiQiY,35
 mimical/utils/filter_set.py,sha256=EITLa2c3FG3n1-v7KatKRwHCRyfZ4TTjsi_WM7Bz64k,6819
-mimical-0.1.0.dist-info/METADATA,sha256=0NZaA2PH7hV235TCt0u_nL5B3GpLHZXWCqFLqLzJRwM,831
-mimical-0.1.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-mimical-0.1.0.dist-info/top_level.txt,sha256=z6HTYpsoNjLUFayXjn8WyjX8C1mIbZw8Arb334cUbwc,8
-mimical-0.1.0.dist-info/RECORD,,
+mimical-0.1.2.dist-info/METADATA,sha256=shzoz1K-wMSdIY0qzujhX7pxsoU6FBqcqy_3hRMgH1o,839
+mimical-0.1.2.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+mimical-0.1.2.dist-info/top_level.txt,sha256=z6HTYpsoNjLUFayXjn8WyjX8C1mIbZw8Arb334cUbwc,8
+mimical-0.1.2.dist-info/RECORD,,

{mimical-0.1.0.dist-info → mimical-0.1.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.9.0)
+Generator: setuptools (80.10.2)
 Root-Is-Purelib: true
 Tag: py3-none-any