pytme 0.3.1__cp311-cp311-macosx_15_0_arm64.whl → 0.3.1.dev20250731__cp311-cp311-macosx_15_0_arm64.whl

pytme-0.3.1.dev20250731.data/scripts/estimate_ram_usage.py

@@ -0,0 +1,97 @@
+#!python
+""" Estimate RAM requirements for template matching jobs.
+
+    Copyright (c) 2023 European Molecular Biology Laboratory
+
+    Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
+"""
+import numpy as np
+import argparse
+from tme import Density
+from tme.matching_utils import estimate_ram_usage
+from tme.matching_exhaustive import MATCHING_EXHAUSTIVE_REGISTER
+
+
+def parse_args():
+    parser = argparse.ArgumentParser(
+        description="Estimate RAM usage for template matching."
+    )
+    parser.add_argument(
+        "-m",
+        "--target",
+        dest="target",
+        type=str,
+        required=True,
+        help="Path to a target in CCP4/MRC format.",
+    )
+    parser.add_argument(
+        "-i",
+        "--template",
+        dest="template",
+        type=str,
+        required=True,
+        help="Path to a template in PDB/MMCIF or CCP4/MRC format.",
+    )
+    parser.add_argument(
+        "--matching_method",
+        required=False,
+        default=None,
+        help="Analyzer method to use.",
+    )
+    parser.add_argument(
+        "-s",
+        dest="score",
+        type=str,
+        default="FLCSphericalMask",
+        help="Template matching scoring function.",
+        choices=MATCHING_EXHAUSTIVE_REGISTER.keys(),
+    )
+    parser.add_argument(
+        "--ncores", type=int, help="Number of cores for parallelization.", required=True
+    )
+    parser.add_argument(
+        "--no_edge_padding",
+        dest="no_edge_padding",
+        action="store_true",
+        default=False,
+        help="Whether to pad the edges of the target. This is useful, if the target"
+        " has a well defined bounding box, e.g. a density map.",
+    )
+    parser.add_argument(
+        "--no_fourier_padding",
+        dest="no_fourier_padding",
+        action="store_true",
+        default=False,
+        help="Whether input arrays should be zero-padded to the full convolution shape"
+        " for numerical stability. When working with very large targets such as"
+        " tomograms it is safe to use this flag and benefit from the performance gain.",
+    )
+    args = parser.parse_args()
+    return args
+
+
+def main():
+    args = parse_args()
+    target = Density.from_file(args.target)
+    template = Density.from_file(args.template)
+
+    target_box = target.shape
+    if not args.no_edge_padding:
+        target_box = np.add(target_box, template.shape)
+
+    template_box = template.shape
+    if args.no_fourier_padding:
+        template_box = np.ones(len(template_box), dtype=int)
+
+    result = estimate_ram_usage(
+        shape1=target_box,
+        shape2=template_box,
+        matching_method=args.score,
+        ncores=args.ncores,
+        analyzer_method="MaxScoreOverRotations",
+    )
+    print(result)
+
+
+if __name__ == "__main__":
+    main()

{pytme-0.3.1.data → pytme-0.3.1.dev20250731.data}/scripts/match_template.py

@@ -359,8 +359,8 @@ def parse_args():
         "--invert-target-contrast",
         action="store_true",
         default=False,
-        help="Invert the target's contrast for cases where templates to-be-matched have "
-        "negative values, e.g. tomograms.",
+        help="Invert the target contrast. Useful for matching on tomograms if the "
+        "template has not been inverted.",
     )
     io_group.add_argument(
         "--scramble-phases",

{pytme-0.3.1.data → pytme-0.3.1.dev20250731.data}/scripts/postprocess.py

@@ -188,7 +188,7 @@ def parse_args():
     )
     additional_group.add_argument(
         "--n-false-positives",
-        type=int,
+        type=float,
         default=None,
         required=False,
         help="Number of accepted false-positives picks to determine minimum score.",
@@ -318,11 +318,7 @@ def normalize_input(foregrounds: Tuple[str], backgrounds: Tuple[str]) -> Tuple:
         data = load_matching_output(foreground)
         scores, _, rotations, rotation_mapping, *_ = data
 
-        # We could normalize to unit sdev, but that might lead to unexpected
-        # results for flat background distributions
-        # scores -= scores.mean()
         indices = tuple(slice(0, x) for x in scores.shape)
-
         indices_update = scores > scores_out[indices]
         scores_out[indices][indices_update] = scores[indices_update]
 
@@ -369,9 +365,7 @@ def normalize_input(foregrounds: Tuple[str], backgrounds: Tuple[str]) -> Tuple:
     scores_norm = np.full(out_shape_norm, fill_value=0, dtype=np.float32)
     for background in backgrounds:
         data_norm = load_matching_output(background)
-
-        scores = data_norm[0]
-        # scores -= scores.mean()
+        scores, _, rotations, rotation_mapping, *_ = data_norm
 
         indices = tuple(slice(0, x) for x in scores.shape)
         indices_update = scores > scores_norm[indices]
@@ -381,9 +375,10 @@ def normalize_input(foregrounds: Tuple[str], backgrounds: Tuple[str]) -> Tuple:
     update = tuple(slice(0, int(x)) for x in np.minimum(out_shape, scores.shape))
     scores_out = np.full(out_shape, fill_value=0, dtype=np.float32)
     scores_out[update] = data[0][update] - scores_norm[update]
+    scores_out = np.fmax(scores_out, 0, out=scores_out)
+    scores_out[update] += scores_norm[update].mean()
 
     # scores_out[update] = np.divide(scores_out[update], 1 - scores_norm[update])
-    scores_out = np.fmax(scores_out, 0, out=scores_out)
     data[0] = scores_out
 
     fg, bg = simple_stats(data[0]), simple_stats(scores_norm)
@@ -485,8 +480,11 @@ def main():
     if orientations is None:
         translations, rotations, scores, details = [], [], [], []
 
-        # Data processed by normalize_input is guaranteed to have this shape
-        scores, offset, rotation_array, rotation_mapping, meta = data
+        var = None
+        # Data processed by normalize_input is guaranteed to have this shape)
+        scores, _, rotation_array, rotation_mapping, *_ = data
+        if len(data) == 6:
+            scores, _, rotation_array, rotation_mapping, var, *_ = data
 
         cropped_shape = np.subtract(
             scores.shape, np.multiply(args.min_boundary_distance, 2)
@@ -509,13 +507,16 @@ def main():
             )
             args.n_false_positives = max(args.n_false_positives, 1)
             n_correlations = np.size(scores[cropped_slice]) * len(rotation_mapping)
+            std = np.std(scores[cropped_slice])
+            if var is not None:
+                std = np.asarray(np.sqrt(var)).reshape(())
+
             minimum_score = np.multiply(
                 erfcinv(2 * args.n_false_positives / n_correlations),
-                np.sqrt(2) * np.std(scores[cropped_slice]),
+                np.sqrt(2) * std,
             )
-            print(f"Determined minimum score cutoff: {minimum_score}.")
-            minimum_score = max(minimum_score, 0)
-            args.min_score = minimum_score
+            print(f"Determined cutoff --min-score {minimum_score}.")
+            args.min_score = max(minimum_score, 0)
 
         args.batch_dims = None
         if hasattr(cli_args, "batch_dims"):

{pytme-0.3.1.data → pytme-0.3.1.dev20250731.data}/scripts/preprocessor_gui.py

@@ -474,6 +474,7 @@ def membrane_mask(
     **kwargs,
 ) -> NDArray:
     return create_mask(
+        center=(center_x, center_y, center_z),
         mask_type="membrane",
         shape=template.shape,
         radius=radius,

{pytme-0.3.1.dist-info → pytme-0.3.1.dev20250731.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pytme
-Version: 0.3.1
+Version: 0.3.1.dev20250731
 Summary: Python Template Matching Engine
 Author: Valentin Maurer
 Author-email: Valentin Maurer <valentin.maurer@embl-hamburg.de>
@@ -26,9 +26,7 @@ Requires-Dist: importlib_resources
 Requires-Dist: joblib
 Provides-Extra: cupy
 Requires-Dist: cupy-cuda12x>13.0.0; extra == "cupy"
-Provides-Extra: cupy-voltools
-Requires-Dist: cupy-cuda12x>13.0.0; extra == "cupy-voltools"
-Requires-Dist: voltools; extra == "cupy-voltools"
+Requires-Dist: voltools; extra == "cupy"
 Provides-Extra: pytorch
 Requires-Dist: torch; extra == "pytorch"
 Requires-Dist: torchvision; extra == "pytorch"

{pytme-0.3.1.dist-info → pytme-0.3.1.dev20250731.dist-info}/RECORD

@@ -1,33 +1,36 @@
-pytme-0.3.1.data/scripts/estimate_memory_usage.py,sha256=Ry46LXUv3SZ0g41g3RDUg9UH6hiSnnG3mHTyaGletXE,2114
-pytme-0.3.1.data/scripts/match_template.py,sha256=X0Sa4dBuE3fvKer--JgY7kPSyZ7H6fa5PKi2lxRoyzM,37563
-pytme-0.3.1.data/scripts/postprocess.py,sha256=0QOUzqa76Wrg7JK51qEtjm7XH78UFdMuDia50HmlXwU,27638
-pytme-0.3.1.data/scripts/preprocess.py,sha256=eq-67cuj3WFx5jAdS56yQSVv_sCt7SRW-dqzQRbLnVE,6328
-pytme-0.3.1.data/scripts/preprocessor_gui.py,sha256=R73N-UTSiAplTqyRw-SLGcGusnJVv2dlAFLuqmUrl-8,44153
-pytme-0.3.1.data/scripts/pytme_runner.py,sha256=dqCd60puAOOOSvuCxrJC1MbfdsRS-ctMso5YIwM-JkI,40356
-pytme-0.3.1.dist-info/licenses/LICENSE,sha256=gXf5dRMhNSbfLPYYTY_5hsZ1r7UU1OaKQEAQUhuIBkM,18092
+pytme-0.3.1.dev20250731.data/scripts/estimate_memory_usage.py,sha256=Ry46LXUv3SZ0g41g3RDUg9UH6hiSnnG3mHTyaGletXE,2114
+pytme-0.3.1.dev20250731.data/scripts/estimate_ram_usage.py,sha256=R1NDpFajcF-MonJ4a43SfDlA-nxBYwK7D2quzCdsVFM,2767
+pytme-0.3.1.dev20250731.data/scripts/match_template.py,sha256=Px443VNaxto_GPuL16d2TcFp7zPrU-camVdGeW4dHNA,37556
+pytme-0.3.1.dev20250731.data/scripts/postprocess.py,sha256=-n7WFjw-AoVe1BLFCgYtfnjdSpZE65o2qeYVmxO_Jh4,27708
+pytme-0.3.1.dev20250731.data/scripts/preprocess.py,sha256=eq-67cuj3WFx5jAdS56yQSVv_sCt7SRW-dqzQRbLnVE,6328
+pytme-0.3.1.dev20250731.data/scripts/preprocessor_gui.py,sha256=fw1Q0G11Eit7TRt9BNqqn5vYthOWt4GdaFS-WfeznbE,44200
+pytme-0.3.1.dev20250731.data/scripts/pytme_runner.py,sha256=dqCd60puAOOOSvuCxrJC1MbfdsRS-ctMso5YIwM-JkI,40356
+pytme-0.3.1.dev20250731.dist-info/licenses/LICENSE,sha256=gXf5dRMhNSbfLPYYTY_5hsZ1r7UU1OaKQEAQUhuIBkM,18092
 scripts/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 scripts/estimate_memory_usage.py,sha256=UiaX30o_H59vzTQZaXISxgzWj5jwgFbMoH1E5ydVHcw,2115
+scripts/estimate_ram_usage.py,sha256=rN7haobnHg3YcgGJIp81FNiCzy8-saJGeEurQlmQmNQ,2768
 scripts/eval.py,sha256=ebJVLxbRlB6TI5YHNr0VavZ4lmaRdf8QVafyiDhh_oU,2528
 scripts/extract_candidates.py,sha256=B2O4Xm0eVJzBZOblfkH5za8fTxLIdBRDl89Qwkq4Kjk,8097
-scripts/match_template.py,sha256=LsoS7gPh6tx3c5uyF3v5XbATjb8jJ_jh91zmO2IruZ0,37564
+scripts/match_template.py,sha256=akKSFalnhsk2OdqELCKFvrBhJ49U_UoWX4xs-42NKAY,37557
+scripts/match_template_devel.py,sha256=JSeJd4L-vVUn4VYOoKms9RvGUKqLf5NTNoviz7F29ns,46599
 scripts/match_template_filters.py,sha256=Gj4a1b_S5NWp_dfFEPFn0D7jGf-qYgBbnTvZZ4bwqOQ,42036
-scripts/postprocess.py,sha256=YNSySz76axtNvz7R5eCvS90eJjtKQQbWMLSexFTkEbg,27639
+scripts/postprocess.py,sha256=_9mFpFQww0TbMQeFaDRxR_AJh2wdGfXrNbqXVUZhtZY,27709
 scripts/preprocess.py,sha256=PrtO0aWGbTvSMqCdNYuzW02FoGvSsvQzJab52DTssQ4,6329
-scripts/preprocessor_gui.py,sha256=eozUE6D_vJOO11Prardwm7zWrjvTXLHFaAMmY7yfNIc,44154
+scripts/preprocessor_gui.py,sha256=GUtq8_jU0NGqTEq5ZyjMaeBskJIxao4rznuraNv_02s,44201
 scripts/pytme_runner.py,sha256=BD5u45vtzJo_d6ZAM2N_CKnGpfjtNg4v7C-31vbTGnU,40357
-scripts/refine_matches.py,sha256=1AG-E2PuTauflR_qVC1CaZKg7ev9xxGu3CIYeyJ2-WQ,12777
+scripts/refine_matches.py,sha256=dLu3aW0-iAn0Qn-GoQBaZfgEGUcTWMQ2J2tA8aNm5Yo,12725
 tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-tests/test_analyzer.py,sha256=HNZf12dZbuMTJ1oYhdDd1nn9NSGXV12ReEqRjNQ96UI,8393
+tests/test_analyzer.py,sha256=9TVJacQF44AnMYOWfLhqQgz1V2TeKjijVT1rJb50NMw,8360
 tests/test_backends.py,sha256=65jCvPfB2YjUHkhmjkC49Rpd1SyPRQ7_lnLXHI5QC-U,17361
 tests/test_density.py,sha256=JVQunV445qij5WdcpKn-5GKqT3endzjXvBPkIaXPADo,18914
-tests/test_extensions.py,sha256=1Zv9dG_dmmC2mlbX91YIPyGLSToPC0202-ffLAfVcr4,5203
+tests/test_extensions.py,sha256=K71MvMhLdZz66ifJYqRl0IEr7-PCXSMxKokg-4NCc8Q,5170
 tests/test_matching_cli.py,sha256=JF7LQixpFQMpbijoPwtNSe9FoYXZmBR6J3T5BvsLbR8,11202
 tests/test_matching_data.py,sha256=U6ISe4lBLDj-OzgA6QAaoO_aegCJjPtXqHbPiPZ2tkA,6091
 tests/test_matching_exhaustive.py,sha256=bRPCN0pyZk3DmXMrWRcEGAksYoch8P7fRiwE3g0yIf4,4039
 tests/test_matching_memory.py,sha256=XrBGRi4cIp3-4nN6s7tj0pBbFJrvJaG3vQdtK-6uzY0,1151
 tests/test_matching_optimization.py,sha256=bYt3d_nHewTRxKCXgGaMLhObkqBufGwrYL4gfinr_jE,7732
 tests/test_matching_utils.py,sha256=m6mkjo-rgA0q67MYQwjeyy_y6GBErh68A-lqxvQ8NT4,4948
-tests/test_orientations.py,sha256=ydqYZc3mOWSweFEGWMrMaygxX7-7in7forUtiNWfQKc,6767
+tests/test_orientations.py,sha256=BnTWHXplucO9_f1TognyZNVQdzGgr1ckt-YGDrlHDcU,6250
 tests/test_parser.py,sha256=57oaksWrKNB4Z_22IxfW0nXMyQWLJFVsuvnJQPhMn10,993
 tests/test_rotations.py,sha256=Kll51PZm_5MWP6TcW_II6oJLgORM4piZtWbzhn2fiA8,5374
 tests/test_structure.py,sha256=Qgrex3wYl9TpFLcqMeUOkq-7w93bzEsMNStKdJdsbnw,8881
@@ -62,16 +65,16 @@ tests/preprocessing/test_utils.py,sha256=RnqlA3vHcVguWp0gmBOwBgUZK85ylNLqr_oFkf8
 tme/__init__.py,sha256=GXfIuzU4fh2KZfgUOIXnNeKlJ8kSp3EqoBr6bSik848,217
 tme/__version__.py,sha256=r4xAFihOf72W9TD-lpMi6ntWSTKTP2SlzKP1ytkjRbI,22
 tme/cli.py,sha256=48Q7QGIuCwNSms5wOnGmWjMSlZrXjAQUz_9zsIFT9tY,3652
-tme/density.py,sha256=iupy3gL7gwE2Q9FHcZfHY_AcbOSUAo3i9tSbC-KF-DA,82405
+tme/density.py,sha256=qYwLi6zuGlSYXP3mQwfahaAVrSolq718sujeK6ZSE1k,84484
 tme/extensions.cpython-311-darwin.so,sha256=xUCjh1eMK3iKWMC04oFG3LzxBRAqHpl7idIIV4ezx3Q,415840
 tme/mask.py,sha256=4xHqWtOabgdYDDCXHpXflaZmLlmE2_9-bxjs4AaCIYM,10472
-tme/matching_data.py,sha256=l9eIJOkANOn-sHWeCVU-1RskMloqH0KmUFQcOQTt6qQ,30361
-tme/matching_exhaustive.py,sha256=YswFCaRTaPaGQVRf7SgrmsqEHlnC83u8G4y-PIlR-8w,18270
+tme/matching_data.py,sha256=y6UBUykYpZHsl5NEDyKthKztuwcKFIaOIlB0eEh-Sww,31255
+tme/matching_exhaustive.py,sha256=DnWl7zBfnK83MFZzLDQ9WsBvI2mZkTikxpiXIWrdmxQ,18385
 tme/matching_optimization.py,sha256=r2zMyOKyvoP8OX9xValJE0DLWbLpNdyY1MLWcOi-H1U,45715
-tme/matching_scores.py,sha256=ZYw7ff0y0Zs6fzUwTCQ34Gth4Ckx2ZV7qNk1bH4NXdw,34849
+tme/matching_scores.py,sha256=sX4hMki9WjwgenNWJ1wNu04J808wOgGuVqbRYSA2TB8,35860
 tme/matching_utils.py,sha256=Qn65B2F8v1yHLetqpiirvUbj-A9-J1giq3lE9cSb-1E,27426
 tme/memory.py,sha256=lOD_XJtAWo3IFG5fJIdYgLSpn8o0ORO6Vua_tlm5YEk,9683
-tme/orientations.py,sha256=93nmt4GPiuBsMWfwSuQVHUBrgY-5k53PlaCaDXZCZjc,21345
+tme/orientations.py,sha256=23HQ2jmW74cAY7RBHe-fB-T1sb8lJ7OfbnP4W5uYZ_M,21857
 tme/parser.py,sha256=d59A7meIUJ8OzfB6eaVqd7CwLj9oYnOfubqlvygbu1U,24210
 tme/preprocessor.py,sha256=7DAGRfCPc9ge-hEuYsNA_KCeajVnpWl-w4NzGQS53GM,40377
 tme/rotations.py,sha256=wVnvZrRCHb1wd5E6yDsLxiP2G0Oin66A4W14vsz4i50,10641
@@ -79,19 +82,19 @@ tme/structure.py,sha256=ojk-IQnIe1JrzxUVHlNlyLxtwzNkNykvxTaXvyBMmbs,72135
 tme/types.py,sha256=NAY7C4qxE6yz-DXVtClMvFfoOV-spWGLNfpLATZ1LcU,442
 tme/analyzer/__init__.py,sha256=aJyVGlQwO6Ij-_NZ5rBlgBQQSIj0dqpUwlmvIvnQqBM,89
 tme/analyzer/_utils.py,sha256=48Xq2Hi_P3VYl1SozYz3WwEj3BwL1QdtFYx7dTxv0bc,6344
-tme/analyzer/aggregation.py,sha256=tl6Vw0VhdhPYwb-Y82eAK83odL2JD0d5C3N39qJRVZM,27875
+tme/analyzer/aggregation.py,sha256=3ieZlNcDp0dhnQ85DdVLsCFrRfqU4jim3JRcMwORF_U,28518
 tme/analyzer/base.py,sha256=2uEYKa0xLwggJUenAA6-l8DIO5sYtklHMg9dR3DzAOI,3887
 tme/analyzer/peaks.py,sha256=y40YVa2zJFLWD3aoP0xtuhK8yOrQV0AVH6ElWyVjXkM,32587
 tme/analyzer/proxy.py,sha256=NH0J93ESl5NAVd_22rLZGDWjCx1ov8I995Fr3mYqUSM,4162
 tme/backends/__init__.py,sha256=VUvEnpfjmZQVn_9QHkLPBoa6y8M3gDyNNL9kq4OQNGE,5249
 tme/backends/_cupy_utils.py,sha256=scxCSK9BcsDaIbHR2mFxAJRIxdc0r5JTC1gCJmVJa64,24558
-tme/backends/_jax_utils.py,sha256=0rybsyG2QbGDdQg-1ruDIt1F15DZcz_TguZYjbepCA4,5838
+tme/backends/_jax_utils.py,sha256=8zJJyUeXAT0txjmiDt_iCsmUMamJQuo4cz1RxE6UO6I,6853
 tme/backends/_numpyfftw_utils.py,sha256=RnYgbSs_sL-NlwYGRqU9kziq0U5qzl9GecVx9uUeSJs,7904
-tme/backends/cupy_backend.py,sha256=G3rsdmxWTes8pM82TTnWvoq1bwGrNsBTbfJMSc5gfTA,8269
-tme/backends/jax_backend.py,sha256=eHN0PvWVpjoKaYUJ0oRcdXwF7muKrgVAUzb96QRDXWI,12069
-tme/backends/matching_backend.py,sha256=oWARMu_Mt6apnvpYGCbQ1_x7tl_PZoxVtVb8HJgtQ-o,32953
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 tme/backends/mlx_backend.py,sha256=3aAKv7VkK_jfxwDMPQZsLp_lRU8MBJ6zNAzrs6VZd3s,6718
-tme/backends/npfftw_backend.py,sha256=P151VbhML5myCMX1o4ArHYRNz_Dz6XoGVyQIesEK2zI,18698
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 tme/backends/pytorch_backend.py,sha256=yn1hhowUMmzMLHdh2jqw2B0CvBIVcSAWOvRMMDkSHmw,14229
 tme/data/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tme/data/c48n309.npy,sha256=NwH64mOEbm3tStq5c98o81fY1vMOoq4nvXDAh7Z7iZg,296768
@@ -126,8 +129,8 @@ tme/filters/ctf.py,sha256=HNB03Pw3gn2Y8pIM2391iRHQzp2NcHZWFDC61v3K0oM,24520
 tme/filters/reconstruction.py,sha256=4gCGpuWuM-yCDQvuzyex_Q8bmsFqUI_8IoZnv3B_3UA,7564
 tme/filters/wedge.py,sha256=JWiN9IwRXnc7A7syq11kSuin6QjhlVmi38nwGHu4yxE,19541
 tme/filters/whitening.py,sha256=Zwk-0jMVqy_F8TdQ0ht5unMz2JBOePOC3okUhQpU0bo,6348
-pytme-0.3.1.dist-info/METADATA,sha256=uGvw-jEiKmPKGI-cQurxjdCgvwrRhcCLZzbIQmF2NqM,5079
-pytme-0.3.1.dist-info/WHEEL,sha256=SPbiHAOPLnBtml4sk5MIwvWF6YnGfOfy9C__W6Bpeg4,109
-pytme-0.3.1.dist-info/entry_points.txt,sha256=pbUSmB0J4Ghlg0w7jHfaFSvPMuvRWzeSuvdjdRPisAU,288
-pytme-0.3.1.dist-info/top_level.txt,sha256=ovCUR7UXXouH3zYt_fJLoqr_vtjp1wudFgjVAnztQLE,18
-pytme-0.3.1.dist-info/RECORD,,
+pytme-0.3.1.dev20250731.dist-info/METADATA,sha256=0wYI-yjiSeP9CdHpoZSjw8X9OCMk80UafjOVxZDB8YA,4991
+pytme-0.3.1.dev20250731.dist-info/WHEEL,sha256=SPbiHAOPLnBtml4sk5MIwvWF6YnGfOfy9C__W6Bpeg4,109
+pytme-0.3.1.dev20250731.dist-info/entry_points.txt,sha256=pbUSmB0J4Ghlg0w7jHfaFSvPMuvRWzeSuvdjdRPisAU,288
+pytme-0.3.1.dev20250731.dist-info/top_level.txt,sha256=ovCUR7UXXouH3zYt_fJLoqr_vtjp1wudFgjVAnztQLE,18
+pytme-0.3.1.dev20250731.dist-info/RECORD,,

scripts/estimate_ram_usage.py

@@ -0,0 +1,97 @@
+#!python3
+""" Estimate RAM requirements for template matching jobs.
+
+    Copyright (c) 2023 European Molecular Biology Laboratory
+
+    Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
+"""
+import numpy as np
+import argparse
+from tme import Density
+from tme.matching_utils import estimate_ram_usage
+from tme.matching_exhaustive import MATCHING_EXHAUSTIVE_REGISTER
+
+
+def parse_args():
+    parser = argparse.ArgumentParser(
+        description="Estimate RAM usage for template matching."
+    )
+    parser.add_argument(
+        "-m",
+        "--target",
+        dest="target",
+        type=str,
+        required=True,
+        help="Path to a target in CCP4/MRC format.",
+    )
+    parser.add_argument(
+        "-i",
+        "--template",
+        dest="template",
+        type=str,
+        required=True,
+        help="Path to a template in PDB/MMCIF or CCP4/MRC format.",
+    )
+    parser.add_argument(
+        "--matching_method",
+        required=False,
+        default=None,
+        help="Analyzer method to use.",
+    )
+    parser.add_argument(
+        "-s",
+        dest="score",
+        type=str,
+        default="FLCSphericalMask",
+        help="Template matching scoring function.",
+        choices=MATCHING_EXHAUSTIVE_REGISTER.keys(),
+    )
+    parser.add_argument(
+        "--ncores", type=int, help="Number of cores for parallelization.", required=True
+    )
+    parser.add_argument(
+        "--no_edge_padding",
+        dest="no_edge_padding",
+        action="store_true",
+        default=False,
+        help="Whether to pad the edges of the target. This is useful, if the target"
+        " has a well defined bounding box, e.g. a density map.",
+    )
+    parser.add_argument(
+        "--no_fourier_padding",
+        dest="no_fourier_padding",
+        action="store_true",
+        default=False,
+        help="Whether input arrays should be zero-padded to the full convolution shape"
+        " for numerical stability. When working with very large targets such as"
+        " tomograms it is safe to use this flag and benefit from the performance gain.",
+    )
+    args = parser.parse_args()
+    return args
+
+
+def main():
+    args = parse_args()
+    target = Density.from_file(args.target)
+    template = Density.from_file(args.template)
+
+    target_box = target.shape
+    if not args.no_edge_padding:
+        target_box = np.add(target_box, template.shape)
+
+    template_box = template.shape
+    if args.no_fourier_padding:
+        template_box = np.ones(len(template_box), dtype=int)
+
+    result = estimate_ram_usage(
+        shape1=target_box,
+        shape2=template_box,
+        matching_method=args.score,
+        ncores=args.ncores,
+        analyzer_method="MaxScoreOverRotations",
+    )
+    print(result)
+
+
+if __name__ == "__main__":
+    main()

scripts/match_template.py

@@ -359,8 +359,8 @@ def parse_args():
         "--invert-target-contrast",
         action="store_true",
         default=False,
-        help="Invert the target's contrast for cases where templates to-be-matched have "
-        "negative values, e.g. tomograms.",
+        help="Invert the target contrast. Useful for matching on tomograms if the "
+        "template has not been inverted.",
     )
     io_group.add_argument(
         "--scramble-phases",