CUQIpy 1.2.0.post0.dev15__py3-none-any.whl → 1.2.0.post0.dev30__py3-none-any.whl

{CUQIpy-1.2.0.post0.dev15.dist-info → CUQIpy-1.2.0.post0.dev30.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: CUQIpy
-Version: 1.2.0.post0.dev15
+Version: 1.2.0.post0.dev30
 Summary: Computational Uncertainty Quantification for Inverse problems in Python
 Maintainer-email: "Nicolai A. B. Riis" <nabr@dtu.dk>, "Jakob S. Jørgensen" <jakj@dtu.dk>, "Amal M. Alghamdi" <amaal@dtu.dk>, Chao Zhang <chaz@dtu.dk>
 License: Apache License
@@ -231,8 +231,9 @@ CUQIpy is part of the [CUQI project](https://www.compute.dtu.dk/english/cuqi) su
 
 - **Papers:** CUQIpy on ArXiv - [Part I](https://arxiv.org/abs/2305.16949) & [Part II](https://arxiv.org/abs/2305.16951)
 
-- **Training:** [Demo & training notebooks](https://github.com/CUQI-DTU/CUQIpy-demos)
+- **CUQI book:** [CUQI book website](https://cuqi-dtu.github.io/CUQI-Book/)
 
+- **User showcases:** [Showcase repository](https://github.com/CUQI-DTU/CUQIpy-User-Showcase/)
 
 ## 🚀 Quickstart
 Install CUQIpy using pip:

{CUQIpy-1.2.0.post0.dev15.dist-info → CUQIpy-1.2.0.post0.dev30.dist-info}/RECORD

@@ -1,6 +1,6 @@
 cuqi/__init__.py,sha256=LsGilhl-hBLEn6Glt8S_l0OJzAA1sKit_rui8h-D-p0,488
 cuqi/_messages.py,sha256=fzEBrZT2kbmfecBBPm7spVu7yHdxGARQB4QzXhJbCJ0,415
-cuqi/_version.py,sha256=jnnRtB8exI7lWU5EPo-fzA3hR7cN_F8fP6jeWSCwWEk,509
+cuqi/_version.py,sha256=QJEhKLIZcwiFhDOxL5fW3HoGva9HIMdu-ceQvUCHsjs,509
 cuqi/config.py,sha256=wcYvz19wkeKW2EKCGIKJiTpWt5kdaxyt4imyRkvtTRA,526
 cuqi/diagnostics.py,sha256=5OrbJeqpynqRXOe5MtOKKhe7EAVdOEpHIqHnlMW9G_c,3029
 cuqi/array/__init__.py,sha256=-EeiaiWGNsE3twRS4dD814BIlfxEsNkTCZUc5gjOXb0,30
@@ -40,13 +40,13 @@ cuqi/experimental/mcmc/_conjugate_approx.py,sha256=uEnY2ea9su5ivcNagyRAwpQP2gBY9
 cuqi/experimental/mcmc/_cwmh.py,sha256=50v3uZaWhlVnfrEB5-lB_7pn8QoUVBe-xWxKGKbmNHg,7234
 cuqi/experimental/mcmc/_direct.py,sha256=9pQS_2Qk2-ybt6m8WTfPoKetcxQ00WaTRN85-Z0FrBY,777
 cuqi/experimental/mcmc/_gibbs.py,sha256=a_Zr007F233R6A3CJ_0zlQppsQrVuX8-oWCbNJWJxmA,12745
-cuqi/experimental/mcmc/_hmc.py,sha256=2MuU-fWvun0bmt1niFLL7iIHbtwubI2b-MHRykWDjwM,19548
+cuqi/experimental/mcmc/_hmc.py,sha256=AR8ucnjPe9Q78em3IMoihLoifdBxu9oAjrQ51AYPHH4,19390
 cuqi/experimental/mcmc/_langevin_algorithm.py,sha256=yNO7ABxmkixzcLG-lv57GOTyeTr7HwFs2DrrhuZW9OI,8398
 cuqi/experimental/mcmc/_laplace_approximation.py,sha256=rdiE3cMQFq6FLQcOQwPpuGIxrTAp3aoGPxMDSdeopV0,5688
 cuqi/experimental/mcmc/_mh.py,sha256=MXo0ahXP4KGFkaY4HtvcBE-TMQzsMlTmLKzSvpz7drU,2941
 cuqi/experimental/mcmc/_pcn.py,sha256=wqJBZLuRFSwxihaI53tumAg6AWVuceLMOmXssTetd1A,3374
 cuqi/experimental/mcmc/_rto.py,sha256=OtzgiYCxDoTdXp7y4mkLa2upj74qadesoqHYpr11ZCg,10061
-cuqi/experimental/mcmc/_sampler.py,sha256=S7sY7ORAPz2d7lvUhCRSg1PCbC745YXn4KVIqRYAZtw,20040
+cuqi/experimental/mcmc/_sampler.py,sha256=lWb0ORdkYcVkZ6G0ypHfmrWXZPfaXnsUj1wAncKxa7g,20339
 cuqi/experimental/mcmc/_utilities.py,sha256=kUzHbhIS3HYZRbneNBK41IogUYX5dS_bJxqEGm7TQBI,525
 cuqi/geometry/__init__.py,sha256=Tz1WGzZBY-QGH3c0GiyKm9XHN8MGGcnU6TUHLZkzB3o,842
 cuqi/geometry/_geometry.py,sha256=SDRZdiN2CIuS591lXxqgFoPWPIpwY-MHk75116QvdYY,46901
@@ -85,8 +85,8 @@ cuqi/testproblem/_testproblem.py,sha256=x769LwwRdJdzIiZkcQUGb_5-vynNTNALXWKato7s
 cuqi/utilities/__init__.py,sha256=H7xpJe2UinjZftKvE2JuXtTi4DqtkR6uIezStAXwfGg,428
 cuqi/utilities/_get_python_variable_name.py,sha256=QwlBVj2koJRA8s8pWd554p7-ElcI7HUwY32HknaR92E,1827
 cuqi/utilities/_utilities.py,sha256=Jc4knn80vLoA7kgw9FzXwKVFGaNBOXiA9kgvltZU3Ao,11777
-CUQIpy-1.2.0.post0.dev15.dist-info/LICENSE,sha256=kJWRPrtRoQoZGXyyvu50Uc91X6_0XRaVfT0YZssicys,10799
-CUQIpy-1.2.0.post0.dev15.dist-info/METADATA,sha256=AjFHjLR2ychxpFCl7bziruEmKwSf0O8mpLd_jHCZ4wg,18410
-CUQIpy-1.2.0.post0.dev15.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
-CUQIpy-1.2.0.post0.dev15.dist-info/top_level.txt,sha256=AgmgMc6TKfPPqbjV0kvAoCBN334i_Lwwojc7HE3ZwD0,5
-CUQIpy-1.2.0.post0.dev15.dist-info/RECORD,,
+CUQIpy-1.2.0.post0.dev30.dist-info/LICENSE,sha256=kJWRPrtRoQoZGXyyvu50Uc91X6_0XRaVfT0YZssicys,10799
+CUQIpy-1.2.0.post0.dev30.dist-info/METADATA,sha256=lPVBe_Ad6ghqiE2CkcVDyABxmJ8Hb610VL0cZSxmVeo,18495
+CUQIpy-1.2.0.post0.dev30.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
+CUQIpy-1.2.0.post0.dev30.dist-info/top_level.txt,sha256=AgmgMc6TKfPPqbjV0kvAoCBN334i_Lwwojc7HE3ZwD0,5
+CUQIpy-1.2.0.post0.dev30.dist-info/RECORD,,

cuqi/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2024-09-30T18:06:47+0200",
+ "date": "2024-10-11T09:05:14+0200",
  "dirty": false,
  "error": null,
- "full-revisionid": "59a6730dfe1227a35a2def467daf63265bdba87f",
- "version": "1.2.0.post0.dev15"
+ "full-revisionid": "e46192df9743f4e53f2ad126462ed1fd95a97dd0",
+ "version": "1.2.0.post0.dev30"
 }
 '''  # END VERSION_JSON
 

cuqi/experimental/mcmc/_hmc.py

@@ -109,10 +109,7 @@ class NUTS(Sampler):
 
     def _initialize(self):
 
-        # Arrays to store acceptance rate
-        self._acc = [None] # Overwrites acc from Sampler. TODO. Check if this is necessary
-
-        self._current_alpha_ratio = np.nan # Current alpha ratio is set to some
+        self._current_alpha_ratio = np.nan # Current alpha ratio will be set to some
                                            # value (other than np.nan) before 
                                            # being used
 
@@ -233,6 +230,7 @@ class NUTS(Sampler):
         r_minus, r_plus = np.copy(r_k), np.copy(r_k)
 
         # run NUTS
+        acc = 0
         while (s == 1) and (j <= self.max_depth):
             # sample a direction
             v = int(2*(np.random.rand() < 0.5)-1)
@@ -260,9 +258,8 @@ class NUTS(Sampler):
                 self.current_point = point_prime
                 self.current_target_logd = logd_prime
                 self.current_target_grad = np.copy(grad_prime)
-                self._acc.append(1)
-            else:
-                self._acc.append(0)
+                acc = 1
+
 
             # update number of particles, tree level, and stopping criterion
             n += n_prime
@@ -280,6 +277,8 @@ class NUTS(Sampler):
         if np.isnan(self.current_target_logd):
             raise NameError('NaN potential func')
 
+        return acc
+
     def tune(self, skip_len, update_count):
         """ adapt epsilon during burn-in using dual averaging"""
         k = update_count+1

cuqi/experimental/mcmc/_sampler.py

@@ -220,7 +220,8 @@ class Sampler(ABC):
         if hasattr(self, "_pre_sample"): self._pre_sample()
 
         # Draw samples
-        for _ in tqdm( range(Ns), "Sample: "):
+        pbar = tqdm(range(Ns), "Sample: ")
+        for idx in pbar:
             
             # Perform one step of the sampler
             acc = self.step()
@@ -229,6 +230,9 @@ class Sampler(ABC):
             self._acc.append(acc)
             self._samples.append(self.current_point)
 
+            # display acc rate at progress bar
+            pbar.set_postfix_str(f"acc rate: {np.mean(self._acc[-1-idx:]):.2%}")
+
             # Add sample to batch
             if batch_size > 0:
                 batch_handler.add_sample(self.current_point)
@@ -260,7 +264,8 @@ class Sampler(ABC):
         if hasattr(self, "_pre_warmup"): self._pre_warmup()
 
         # Draw warmup samples with tuning
-        for idx in tqdm(range(Nb), "Warmup: "):
+        pbar = tqdm(range(Nb), "Warmup: ")
+        for idx in pbar:
 
             # Perform one step of the sampler
             acc = self.step()
@@ -273,6 +278,9 @@ class Sampler(ABC):
             self._acc.append(acc)
             self._samples.append(self.current_point)
 
+            # display acc rate at progress bar
+            pbar.set_postfix_str(f"acc rate: {np.mean(self._acc[-1-idx:]):.2%}")
+
             # Call callback function if specified
             self._call_callback(self.current_point, len(self._samples)-1)