pytme 0.2.9__cp311-cp311-macosx_15_0_arm64.whl → 0.2.9.post1__cp311-cp311-macosx_15_0_arm64.whl

{pytme-0.2.9.dist-info → pytme-0.2.9.post1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pytme
-Version: 0.2.9
+Version: 0.2.9.post1
 Summary: Python Template Matching Engine
 Author: Valentin Maurer
 Author-email: Valentin Maurer <valentin.maurer@embl-hamburg.de>
@@ -18,6 +18,7 @@ Requires-Dist: pyfftw>=0.13.1
 Requires-Dist: pytest>=6.2.5
 Requires-Dist: PyYAML>=6.0
 Requires-Dist: scikit-image>=0.19.0
+Requires-Dist: scikit_learn>=1.2.1
 Requires-Dist: pybind11
 Requires-Dist: psutil
 Requires-Dist: h5py

{pytme-0.2.9.dist-info → pytme-0.2.9.post1.dist-info}/RECORD

@@ -1,9 +1,9 @@
-pytme-0.2.9.data/scripts/estimate_ram_usage.py,sha256=R1NDpFajcF-MonJ4a43SfDlA-nxBYwK7D2quzCdsVFM,2767
-pytme-0.2.9.data/scripts/match_template.py,sha256=k_PACJyQfVBwB7zJiFvkurTtsnej_h6LEnvajZjJkus,39558
-pytme-0.2.9.data/scripts/postprocess.py,sha256=Wlbn284vN-Jjo2qpzNNsnW0zOHHHGLQEMeQp5RQJjZk,22759
-pytme-0.2.9.data/scripts/preprocess.py,sha256=7NJRUmPGaSFpGSA5C8f4JUzajRo6alMJ4aEprIyS0oo,6512
-pytme-0.2.9.data/scripts/preprocessor_gui.py,sha256=2b_xqZwEdB7GKmwWGu5Z4qewN71XZcEa1OVTe-15YF0,41789
-pytme-0.2.9.dist-info/licenses/LICENSE,sha256=K1IUNSVAz8BXbpH5EA8y5FpaHdvFXnAF2zeK95Lr2bY,18467
+pytme-0.2.9.post1.data/scripts/estimate_ram_usage.py,sha256=R1NDpFajcF-MonJ4a43SfDlA-nxBYwK7D2quzCdsVFM,2767
+pytme-0.2.9.post1.data/scripts/match_template.py,sha256=k_PACJyQfVBwB7zJiFvkurTtsnej_h6LEnvajZjJkus,39558
+pytme-0.2.9.post1.data/scripts/postprocess.py,sha256=Wlbn284vN-Jjo2qpzNNsnW0zOHHHGLQEMeQp5RQJjZk,22759
+pytme-0.2.9.post1.data/scripts/preprocess.py,sha256=7NJRUmPGaSFpGSA5C8f4JUzajRo6alMJ4aEprIyS0oo,6512
+pytme-0.2.9.post1.data/scripts/preprocessor_gui.py,sha256=2b_xqZwEdB7GKmwWGu5Z4qewN71XZcEa1OVTe-15YF0,41789
+pytme-0.2.9.post1.dist-info/licenses/LICENSE,sha256=K1IUNSVAz8BXbpH5EA8y5FpaHdvFXnAF2zeK95Lr2bY,18467
 scripts/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 scripts/estimate_ram_usage.py,sha256=rN7haobnHg3YcgGJIp81FNiCzy8-saJGeEurQlmQmNQ,2768
 scripts/match_template.py,sha256=8OkGMpvJe35mNVP9EMRd1KOTTrvMm9xB0OHLVkNlTV4,39559
@@ -15,7 +15,7 @@ tests/test_analyzer.py,sha256=fMuY0WCh1_D1XdzaryKzq3Mj9Q3pJFpWCNeEO-DYY20,7949
 tests/test_backends.py,sha256=29HlacgrX4fRjFXfzNNh3yDjqHRd7WvCFpTpRQwAsmA,17541
 tests/test_density.py,sha256=vzzy0Gk3uUR096aZgA-e5gOfLnw9qG3RH-xyXtHCO_I,18971
 tests/test_extensions.py,sha256=1Zv9dG_dmmC2mlbX91YIPyGLSToPC0202-ffLAfVcr4,5203
-tests/test_matching_cli.py,sha256=oX8d4QrMJfVu9IJN1BnEeSLvbd4T9iioiidCcrGp5Mk,9307
+tests/test_matching_cli.py,sha256=VoGVi4QhakccVbC3pIQzEwaL97Zgi2Ll4np1zVqdpvo,9345
 tests/test_matching_data.py,sha256=TyvnSJPzdLPiXYWdz9coQ-m4H1tUS_cbD0WaBdvrevg,6062
 tests/test_matching_exhaustive.py,sha256=2_uG8Ir8QUyvGXMHcsBRdvr27j83cgpd53FnRyIkF8M,4055
 tests/test_matching_memory.py,sha256=XrBGRi4cIp3-4nN6s7tj0pBbFJrvJaG3vQdtK-6uzY0,1151
@@ -58,7 +58,7 @@ tme/matching_data.py,sha256=hhtjQl_EimGGmyR2DHiZi82Aeq3xmNF98koevZT7mKc,31238
 tme/matching_exhaustive.py,sha256=VXWOMaLF9m_31d9Hy3mn-PuUBJ0zgsTRb5v4sdRvJPU,18817
 tme/matching_optimization.py,sha256=wQ8k1VBK74twymogr_1LIOjNlhr_Nyl8CN4XxjEADHQ,45688
 tme/matching_scores.py,sha256=A8558Yj1lCEbcLYeevoVXMfhO3jILZeO3ztgp8gA9Xo,41023
-tme/matching_utils.py,sha256=nNOyVs-V8R63P3ma5tXiBS7vDLoNdLv_a0kil43gMTM,37405
+tme/matching_utils.py,sha256=Oa7ytvvaSyck6PSci3XBoakgz8-9tL8Qtv2Sx7P3pVo,36362
 tme/memory.py,sha256=gRKOsputjOjpVhqgrLn2q8JfSCiXGtRdV8wd9XG_Fho,9687
 tme/orientations.py,sha256=yQKJaYQWkBqDOIYFmVDP47rjdvqwoAHBCvmpu36qoOo,21023
 tme/parser.py,sha256=bqgJ9FPecbnvqFF-xZhRZOwPxawtMqs69SEGS3oaxWQ,21565
@@ -68,8 +68,8 @@ tme/structure.py,sha256=EktAzR_t0cK5J0iBiWlDDGw1okFoiEQgwACAIRDNdgY,72143
 tme/types.py,sha256=NAY7C4qxE6yz-DXVtClMvFfoOV-spWGLNfpLATZ1LcU,442
 tme/analyzer/__init__.py,sha256=DgEulEr9nERtXttTpmEeL8pNLCW-OxGWB4PMMCQ0INs,48
 tme/analyzer/_utils.py,sha256=ioG90NdGGyjC1bXLu9cdBSPFStOG2n5GlPOeS_0SFGs,6083
-tme/analyzer/aggregation.py,sha256=uFE5YNEn2RqOdbTIaTR3KshSp1TTe_6E7mNZ1_HNXW4,21103
-tme/analyzer/peaks.py,sha256=pyoYyt_9k8BcK5hFuxW5ENA8yH0P7DD_GgAwZdHJOOo,32955
+tme/analyzer/aggregation.py,sha256=NYk9EWr670GmYO0gTJ5AalpCbDh30SEAfoA59m6IMGA,21104
+tme/analyzer/peaks.py,sha256=dVIJ1zCT7XPJSVK368uFdVcj7DcwRJYKJQbG9VhEDbQ,33028
 tme/backends/__init__.py,sha256=iGTq1c9CR0ZCAj9uOY6DzqPePYG0ZVvv637FukH-I7I,5257
 tme/backends/_cupy_utils.py,sha256=tzfoR-WyHViSY1E39mKoO5os-1L8zpChIdbf52QN0t4,24650
 tme/backends/_jax_utils.py,sha256=Bo47XU338rNdJ-BNLR4XKmbnnlAz8zxeLQomTNhgLmk,5907
@@ -112,8 +112,8 @@ tme/filters/ctf.py,sha256=ymOi90sf-bSPfHFpdvMPeEsoDHgOerMjH6q1sRNlNiY,14801
 tme/filters/reconstruction.py,sha256=oomYOtWGiw7DXs_NVnQxPVv8zK8hwXZTONiwaFQNTE8,5436
 tme/filters/wedge.py,sha256=t9LKPydjyuhtY9NtkiQug-S5bGt2DDTBAaeNDbH5T9E,17583
 tme/filters/whitening.py,sha256=Rhr-sxxvAVp60yUieiyL96iJcDasbdgq9q1iTtCxS1w,6324
-pytme-0.2.9.dist-info/METADATA,sha256=h8JMb_AIfivw8nUntzAw48jKUaVDvsgmQkojRk3NOZk,5333
-pytme-0.2.9.dist-info/WHEEL,sha256=SPbiHAOPLnBtml4sk5MIwvWF6YnGfOfy9C__W6Bpeg4,109
-pytme-0.2.9.dist-info/entry_points.txt,sha256=ff3LQL3FCWfCYOwFiP9zatm7laUbnwCkuPELkQVyUO4,241
-pytme-0.2.9.dist-info/top_level.txt,sha256=ovCUR7UXXouH3zYt_fJLoqr_vtjp1wudFgjVAnztQLE,18
-pytme-0.2.9.dist-info/RECORD,,
+pytme-0.2.9.post1.dist-info/METADATA,sha256=iRWxbDR6p4Lq4q2PbfXzscjDDxGjMe46KItWTvdbTHA,5374
+pytme-0.2.9.post1.dist-info/WHEEL,sha256=SPbiHAOPLnBtml4sk5MIwvWF6YnGfOfy9C__W6Bpeg4,109
+pytme-0.2.9.post1.dist-info/entry_points.txt,sha256=ff3LQL3FCWfCYOwFiP9zatm7laUbnwCkuPELkQVyUO4,241
+pytme-0.2.9.post1.dist-info/top_level.txt,sha256=ovCUR7UXXouH3zYt_fJLoqr_vtjp1wudFgjVAnztQLE,18
+pytme-0.2.9.post1.dist-info/RECORD,,

tests/test_matching_cli.py

@@ -252,6 +252,7 @@ class TestPostprocessing(TestMatchTemplate):
         }
         cmd = argdict_to_command(argdict, executable="postprocess.py")
         ret = subprocess.run(cmd, capture_output=True, shell=True)
+        print(ret.stdout, ret.stderr)
 
         match output_format:
             case "orientations":

tme/analyzer/aggregation.py

@@ -398,6 +398,7 @@ class MaxScoreOverRotations:
         """Boolean indicating whether class instance can be shared across processes."""
         return True
 
+
 class MaxScoreOverTranslations(MaxScoreOverRotations):
     """
     Determine the translation maximizing the score over all possible rotations.

tme/analyzer/peaks.py

@@ -197,6 +197,9 @@ class PeakCaller(ABC):
         self.rotations = be.full(
             (num_peaks, ndim, ndim), fill_value=0, dtype=be._float_dtype
         )
+        for i in range(ndim):
+            self.rotations[:, i, i] = 1.0
+
         self.scores = be.full((num_peaks,), fill_value=0, dtype=be._float_dtype)
         self.details = be.full((num_peaks,), fill_value=0, dtype=be._float_dtype)
 

tme/matching_utils.py

@@ -15,7 +15,6 @@ from concurrent.futures import ThreadPoolExecutor
 from typing import Tuple, Dict, Callable, Optional
 
 import numpy as np
-from tqdm import tqdm
 from scipy.spatial import ConvexHull
 from scipy.ndimage import gaussian_filter
 
@@ -1151,38 +1150,3 @@ def compute_extraction_box(
     keep = be.multiply(keep, clamp_change == 0)
 
     return obs_beg_clamp, obs_end_clamp, cand_beg, cand_end, keep
-
-
-class TqdmParallel(Parallel):
-    """
-    A minimal Parallel implementation using tqdm for progress reporting.
-
-    Parameters:
-    -----------
-    tqdm_args : dict, optional
-        Dictionary of arguments passed to tqdm.tqdm
-    *args, **kwargs:
-        Arguments to pass to joblib.Parallel
-    """
-
-    def __init__(self, tqdm_args: Dict = {}, *args, **kwargs):
-        super().__init__(*args, **kwargs)
-        self.pbar = tqdm(**tqdm_args)
-
-    def __call__(self, iterable, *args, **kwargs):
-        self.n_tasks = len(iterable) if hasattr(iterable, "__len__") else None
-        return super().__call__(iterable, *args, **kwargs)
-
-    def print_progress(self):
-        if self.n_tasks is None:
-            return super().print_progress()
-
-        if self.n_tasks != self.pbar.total:
-            self.pbar.total = self.n_tasks
-            self.pbar.refresh()
-
-        self.pbar.n = self.n_completed_tasks
-        self.pbar.refresh()
-
-        if self.n_completed_tasks >= self.n_tasks:
-            self.pbar.close()