pytme 0.2.9.post1__cp311-cp311-macosx_15_0_arm64.whl → 0.3b0__cp311-cp311-macosx_15_0_arm64.whl

{pytme-0.2.9.post1.data → pytme-0.3b0.data}/scripts/preprocessor_gui.py

@@ -1,9 +1,10 @@
 #!python
-""" GUI for identifying adequate template matching filter and masks.
+"""
+GUI for identifying suitable masks and analyzing template matchign results.
 
-    Copyright (c) 2023 European Molecular Biology Laboratory
+Copyright (c) 2023 European Molecular Biology Laboratory
 
-    Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
+Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
 """
 import inspect
 import argparse
@@ -23,9 +24,9 @@ from napari.utils.events import EventedList
 
 from tme.backends import backend
 from tme.rotations import align_vectors
-from tme.filters import BandPassFilter, CTF
 from tme import Preprocessor, Density, Orientations
 from tme.matching_utils import create_mask, load_pickle
+from tme.filters import BandPassFilter, CTFReconstructed
 
 preprocessor = Preprocessor()
 SLIDER_MIN, SLIDER_MAX = 0, 25
@@ -71,15 +72,14 @@ def ctf_filter(
     fast_shape = [next_fast_len(x) for x in np.multiply(template.shape, 2)]
     template_pad = backend.topleft_pad(template, fast_shape)
     template_ft = np.fft.rfftn(template_pad, s=template_pad.shape)
-    ctf = CTF(
-        angles=[0],
+    ctf = CTFReconstructed(
         shape=fast_shape,
         defocus_x=[defocus_angstrom],
         acceleration_voltage=acceleration_voltage * 1e3,
         spherical_aberration=spherical_aberration * 1e7,
         amplitude_contrast=amplitude_contrast,
-        phase_shift=[phase_shift],
-        defocus_angle=[defocus_angle],
+        phase_shift=phase_shift,
+        defocus_angle=defocus_angle,
         sampling_rate=np.max(sampling_rate),
         return_real_fourier=True,
         flip_phase=flip_phase,
@@ -1216,7 +1216,8 @@ def main():
 
 def parse_args():
     parser = argparse.ArgumentParser(
-        description="GUI for preparing and analyzing template matching runs."
+        description="GUI for preparing and analyzing template matching runs.",
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
     )
     args = parser.parse_args()
     return args

{pytme-0.2.9.post1.dist-info → pytme-0.3b0.dist-info}/METADATA

@@ -1,10 +1,10 @@
 Metadata-Version: 2.4
 Name: pytme
-Version: 0.2.9.post1
+Version: 0.3b0
 Summary: Python Template Matching Engine
 Author: Valentin Maurer
 Author-email: Valentin Maurer <valentin.maurer@embl-hamburg.de>
-License: Proprietary
+License-Expression: GPL-2.0-only
 Project-URL: Homepage, https://github.com/KosinskiLab/pyTME
 Classifier: Programming Language :: Python :: 3
 Classifier: Operating System :: OS Independent
@@ -12,7 +12,7 @@ Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: mrcfile>=1.4.3
-Requires-Dist: numpy<2.0,>=1.22.2
+Requires-Dist: numpy>=1.22.2
 Requires-Dist: scipy>=1.9.1
 Requires-Dist: pyfftw>=0.13.1
 Requires-Dist: pytest>=6.2.5
@@ -25,19 +25,20 @@ Requires-Dist: h5py
 Requires-Dist: importlib_resources
 Requires-Dist: joblib
 Provides-Extra: cupy
-Requires-Dist: cupy-cuda12x; extra == "cupy"
-Requires-Dist: voltools==0.6.0; extra == "cupy"
+Requires-Dist: cupy-cuda12x>=13.0.0; extra == "cupy"
 Provides-Extra: pytorch
 Requires-Dist: torch; extra == "pytorch"
 Requires-Dist: torchvision; extra == "pytorch"
 Provides-Extra: jax
-Requires-Dist: jax; extra == "jax"
+Requires-Dist: jax[cuda12]; extra == "jax"
 Requires-Dist: jaxlib; extra == "jax"
+Provides-Extra: jax-cpu
+Requires-Dist: jax; extra == "jax-cpu"
+Requires-Dist: jaxlib; extra == "jax-cpu"
 Provides-Extra: all
-Requires-Dist: cupy; extra == "all"
-Requires-Dist: voltools==0.6.0; extra == "all"
+Requires-Dist: cupy-cuda12x>=13.0.0; extra == "all"
 Requires-Dist: torch; extra == "all"
-Requires-Dist: jax; extra == "all"
+Requires-Dist: jax[cuda12]; extra == "all"
 Requires-Dist: jaxlib; extra == "all"
 Requires-Dist: tifffile; extra == "all"
 Dynamic: author

{pytme-0.2.9.post1.dist-info → pytme-0.3b0.dist-info}/RECORD

@@ -1,27 +1,29 @@
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-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
+pytme-0.3b0.data/scripts/estimate_memory_usage.py,sha256=ymDHkRcoFn0eXVHgJu3xh-y4bad5RV3CktH_v5lnDrI,2210
+pytme-0.3b0.data/scripts/match_template.py,sha256=_BSf2aCnJKYz0PKfagIUwFI4i8sFegWsvz-FSb99jp0,39405
+pytme-0.3b0.data/scripts/postprocess.py,sha256=itLpTUe6PtVPjJerL2ajsi4JFbi9n1Wqr8tN9H0z-BU,26964
+pytme-0.3b0.data/scripts/preprocess.py,sha256=Xq9e0on55QeWlAL-Eqo_NQZ2NXznUcj_19qKfIMdNVo,6686
+pytme-0.3b0.data/scripts/preprocessor_gui.py,sha256=gI4FrDOL0qDHdljZ8FWJ8J5V-nV6qccV0szfk4uwo6w,41859
+pytme-0.3b0.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
-scripts/postprocess.py,sha256=TnmNY6b2GUOr_dZoi1F71TPpOzyhffmUULRs79LLefQ,22760
-scripts/preprocess.py,sha256=GP8lPh_rqFv_CDkPTeFbve_tC1Y7KQZl1YrD9w9wvT4,6513
-scripts/preprocessor_gui.py,sha256=8P-xhufzTeH0qEH08ZbF9onHFTq-5FinnhNaNbEv8Lg,41790
+scripts/estimate_memory_usage.py,sha256=pAtEx0TRVjAPmd_Ea0-G4oICUyVdJGM03FgynjBBDPE,2211
+scripts/extract_candidates.py,sha256=GnJb7LI0z2UpMvOS3uY6oIXUJ90R4f2V1jPK5SvJbXg,7246
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+scripts/refine_matches.py,sha256=Y17Ku_t0W9vglPNF2oU5EFrqoedJIm3lCGl-hXRHvjc,21920
 tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-tests/test_analyzer.py,sha256=fMuY0WCh1_D1XdzaryKzq3Mj9Q3pJFpWCNeEO-DYY20,7949
+tests/test_analyzer.py,sha256=FczMo_S3Y1cIn4Z-U-iT_gsNTt9PJXYlIyvv3MX9i6o,8611
 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=VoGVi4QhakccVbC3pIQzEwaL97Zgi2Ll4np1zVqdpvo,9345
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 tests/test_matching_data.py,sha256=TyvnSJPzdLPiXYWdz9coQ-m4H1tUS_cbD0WaBdvrevg,6062
-tests/test_matching_exhaustive.py,sha256=2_uG8Ir8QUyvGXMHcsBRdvr27j83cgpd53FnRyIkF8M,4055
+tests/test_matching_exhaustive.py,sha256=bRPCN0pyZk3DmXMrWRcEGAksYoch8P7fRiwE3g0yIf4,4039
 tests/test_matching_memory.py,sha256=XrBGRi4cIp3-4nN6s7tj0pBbFJrvJaG3vQdtK-6uzY0,1151
-tests/test_matching_optimization.py,sha256=KBmFojKpr1iC_T90vpsrvZoEeFzI41xmejC-WuINZGU,7941
+tests/test_matching_optimization.py,sha256=bYt3d_nHewTRxKCXgGaMLhObkqBufGwrYL4gfinr_jE,7732
 tests/test_matching_utils.py,sha256=9wJPKh5LF_Vb75pKbXy-JT8u_FGLfWioA7nFcOkAto4,6356
-tests/test_orientations.py,sha256=HtCYJB_XGMLjWEvTfCXSxKpE_FvrGg5Uk39dn1zB-4g,6837
+tests/test_orientations.py,sha256=ydqYZc3mOWSweFEGWMrMaygxX7-7in7forUtiNWfQKc,6767
 tests/test_parser.py,sha256=57oaksWrKNB4Z_22IxfW0nXMyQWLJFVsuvnJQPhMn10,993
 tests/test_rotations.py,sha256=CTEkpO8Z-6afgCIk2wGexXBaOqUeGJL2-krm1z4YRFY,5358
 tests/test_structure.py,sha256=Qgrex3wYl9TpFLcqMeUOkq-7w93bzEsMNStKdJdsbnw,8881
@@ -35,10 +37,8 @@ tests/data/Blurring/localgaussian_sigma0510.npy,sha256=KXASnlhxAnvvcgIDCniIHkak-
 tests/data/Blurring/mean_size5.npy,sha256=2APwsCR_1fpwGIc_mG0dPegpcbgXhUbcEEeQo9Wa1iA,42688
 tests/data/Blurring/ntree_sigma0510.npy,sha256=HxYh_ItxdKulp8UiPMzQ0ze2iiQ3Oi7seWFvEzO1kWQ,21408
 tests/data/Blurring/rank_rank3.npy,sha256=MxCsomoNPmiV0Cd-5nl2S8TYCfLyEj-WV19gLH_xe0c,21408
-tests/data/Maps/.DS_Store,sha256=1lFlJ5EFymdzGAUAaI30vcaaLHt3F1LwpG7xILf9jsM,6148
 tests/data/Maps/emd_8621.mrc.gz,sha256=ZAlSOQRT9B_e8xpeodio9j0WBzygl2R1ctg9m8QhCRA,4572566
 tests/data/Raw/em_map.map,sha256=YeY_R0p-90-oZgxfbKGIsyE5bui_uWq9iGhWl0bLYZI,22304
-tests/data/Structures/.DS_Store,sha256=1lFlJ5EFymdzGAUAaI30vcaaLHt3F1LwpG7xILf9jsM,6148
 tests/data/Structures/1pdj.cif,sha256=QdO4e2ulO621PVoK3q9n0qDPDKnzJpV6sPeG6zQec1A,169343
 tests/data/Structures/1pdj.pdb,sha256=nTFGjecultoXNVUBDdsyho0CEzX5i1fSo_aBYDh5-pU,115749
 tests/data/Structures/5khe.cif,sha256=SnC0so37wyuoYwAX5UDTTLvQiknZXxeJrvkGai-11rw,214644
@@ -47,38 +47,41 @@ tests/data/Structures/5khe.pdb,sha256=AjXInxR_DgglZATzSNgB1rs7-LgAn2G1NdgnHb6fAm
 tests/data/Structures/5uz4.cif,sha256=KIcBaOf-RvOV4VRl1AU_EK4BsMxGXS8s8_UdlIhyeWk,6079401
 tests/preprocessing/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tests/preprocessing/test_compose.py,sha256=z44fgQhxJU0-zHSV0CLBMEJqwhK5gEFDhUCLuVsQpQc,2490
-tests/preprocessing/test_frequency_filters.py,sha256=rFms5nQb6KzxQE2IvMu37u8f15kTcN5tD7gr3v5Z-Jo,6610
+tests/preprocessing/test_frequency_filters.py,sha256=EDSkQ8si5mZDEA8edqGBZSdTuooExjICSt5jGoOk3Ko,6705
 tests/preprocessing/test_preprocessor.py,sha256=XyR4xc4YM76PUKuTIiive76Q85DdcyDAvbXNGcoKL8w,4820
 tests/preprocessing/test_utils.py,sha256=2V1a9XtFZYmCyQzgsj0qWzWuXg-JAsOoG5_rtTwxvGg,3031
 tme/__init__.py,sha256=GXfIuzU4fh2KZfgUOIXnNeKlJ8kSp3EqoBr6bSik848,217
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 tme/extensions.cpython-311-darwin.so,sha256=vNaZYhhSrVlCjBlj5nzpKcnnJ_L_-84WhTRz2kWYK2Y,395696
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 tme/types.py,sha256=NAY7C4qxE6yz-DXVtClMvFfoOV-spWGLNfpLATZ1LcU,442
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 tme/data/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tme/data/c48n309.npy,sha256=NwH64mOEbm3tStq5c98o81fY1vMOoq4nvXDAh7Z7iZg,296768
 tme/data/c48n527.npy,sha256=saSUMTa1R0MisPvgFL02a7IHQSwEZ-mJu0v3qJjg5AU,506048
@@ -104,16 +107,16 @@ tme/data/metadata.yaml,sha256=fAgX-mEzB0QMHTEtYDG4cSMbJhYxBbDJH3sdvJvL7a8,750
 tme/data/quat_to_numpy.py,sha256=-gkDZb10fKBxwfYrSLCUWvMB76TzZWELCeKsYProwws,1333
 tme/data/scattering_factors.pickle,sha256=ZHktBc_AlS4H6uoER8AMmn5zOgjBwzgC92hUyww3Nik,38669
 tme/external/bindings.cpp,sha256=CIukugVf55LicY2uSCasHWQlrlO9GS2iUuCR3WLvncM,12912
-tme/filters/__init__.py,sha256=iCPAyxlXtvZdinMKk_nDzk8Ew8K9NkhMFDs1JF5_zEM,243
-tme/filters/_utils.py,sha256=rrgWXdlF8rbAdhQwXcDn3EPE5euhtr1uJDJeqMFmNmI,10106
-tme/filters/bandpass.py,sha256=YygCDFG5d3VZkoX5IxZwmjVgrVnQwyh9p3G-aeaanqo,7795
-tme/filters/compose.py,sha256=czOBaihYcRYKrfNFAAEodurtEYg3SF0PFPMLkCqR8tk,1992
-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.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,,
+tme/filters/__init__.py,sha256=URdfFWPJrgHIHPbWZYkOV6BN4xTAOU41vMENyxgxxRw,261
+tme/filters/_utils.py,sha256=apH5Qgd3-YTA0a4DWPcsC0eg5zunqoVbMbCjPlbYupY,10098
+tme/filters/bandpass.py,sha256=7y0-7K8QNWDKVsHHWKjldk0CNgZjv8f5F7fmI0kvqZo,7837
+tme/filters/compose.py,sha256=yeC84D0HznqhRJ7guV6Cpxzq2UWpvV6nouhFECjIDEw,1980
+tme/filters/ctf.py,sha256=6NHOksV1yEs0KvG_nC5avdkhnJ0yVMJraGASYC4On4Y,21702
+tme/filters/reconstruction.py,sha256=BHcKPuz67tCS7wgoIzAihMiTNPuFAmKZfqIOBIlZoBA,6595
+tme/filters/wedge.py,sha256=bLawfE_oHWB1VvFpjb49GTkvxttq_FNLNWsvo4t1bCk,19920
+tme/filters/whitening.py,sha256=Wcepxg75M3hNtQ3NjCTdyjesZym3Cc52OAxztFdLsiE,6440
+pytme-0.3b0.dist-info/METADATA,sha256=lj3LgLZPoZf0yU_gMIXF-yLqFH4E--l8hiv2MhtksEA,5425
+pytme-0.3b0.dist-info/WHEEL,sha256=SPbiHAOPLnBtml4sk5MIwvWF6YnGfOfy9C__W6Bpeg4,109
+pytme-0.3b0.dist-info/entry_points.txt,sha256=elQ5JqLhmA3XX51WGIkm7hEdB_saxXKVMjqKqdHl--A,247
+pytme-0.3b0.dist-info/top_level.txt,sha256=ovCUR7UXXouH3zYt_fJLoqr_vtjp1wudFgjVAnztQLE,18
+pytme-0.3b0.dist-info/RECORD,,

{pytme-0.2.9.post1.dist-info → pytme-0.3b0.dist-info}/entry_points.txt

@@ -1,5 +1,5 @@
 [console_scripts]
-estimate_ram_usage = scripts:estimate_ram_usage.main
+estimate_memory_usage = scripts:estimate_memory_usage.main
 match_template = scripts:match_template.main
 postprocess = scripts:postprocess.main
 preprocess = scripts:preprocess.main

scripts/{estimate_ram_usage.py → estimate_memory_usage.py}

@@ -1,20 +1,21 @@
 #!python3
-""" Estimate RAM requirements for template matching jobs.
+"""Estimate memory requirements for template matching jobs.
 
-    Copyright (c) 2023 European Molecular Biology Laboratory
+Copyright (c) 2023 European Molecular Biology Laboratory
 
-    Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
+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.memory import estimate_memory_usage
 from tme.matching_exhaustive import MATCHING_EXHAUSTIVE_REGISTER
 
 
 def parse_args():
     parser = argparse.ArgumentParser(
-        description="Estimate RAM usage for template matching."
+        description="Estimate memory usage for template matching.",
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
     )
     parser.add_argument(
         "-m",
@@ -32,14 +33,9 @@ def parse_args():
         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",
+        "--score",
         dest="score",
         type=str,
         default="FLCSphericalMask",
@@ -50,21 +46,12 @@ def parse_args():
         "--ncores", type=int, help="Number of cores for parallelization.", required=True
     )
     parser.add_argument(
-        "--no_edge_padding",
-        dest="no_edge_padding",
+        "--pad_edges",
+        dest="pad_edges",
         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.",
+        help="Whether to pad the edges of the target. Useful if the target does not "
+        "a well-defined bounding box. Defaults to True if splitting is required.",
     )
     args = parser.parse_args()
     return args
@@ -72,19 +59,15 @@ def parse_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)
+    target = Density.from_file(args.target, use_memmap=True)
+    template = Density.from_file(args.template, use_memmap=True)
 
     template_box = template.shape
-    if args.no_fourier_padding:
+    if not args.pad_edges:
         template_box = np.ones(len(template_box), dtype=int)
 
-    result = estimate_ram_usage(
-        shape1=target_box,
+    result = estimate_memory_usage(
+        shape1=target.shape,
         shape2=template_box,
         matching_method=args.score,
         ncores=args.ncores,

scripts/extract_candidates.py

@@ -0,0 +1,224 @@
+#!python3
+""" Prepare orientations stack for refinement.
+
+    Copyright (c) 2023 European Molecular Biology Laboratory
+
+    Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
+"""
+import argparse
+from os.path import splitext
+
+import numpy as np
+
+from tme import Density, Orientations
+from tme.matching_utils import (
+    generate_tempfile_name,
+    rotation_aligning_vectors,
+    euler_from_rotationmatrix,
+    euler_to_rotationmatrix,
+)
+
+
+class ProgressBar:
+    """
+    ASCII progress bar.
+    """
+
+    def __init__(self, message: str, nchars: int, total: int):
+        self._size = nchars - len(message) - (len(str(total))+2) * 2
+        self._message = message
+        self._total = total
+
+    def update(self, cur):
+        x = int(cur * self._size / self._total)
+        print(
+            "%s[%s%s] %i/%i\r"
+            % (self._message, "#" * x, "." * (self._size - x), cur, self._total),
+            end="",
+        )
+
+
+def parse_args():
+    parser = argparse.ArgumentParser(
+        description="Extract matching candidates for further refinement.",
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+    )
+
+    io_group = parser.add_argument_group("Input / Output")
+    io_group.add_argument(
+        "--target",
+        required=True,
+        type=str,
+        help="Extract candidates from this target.",
+    )
+    io_group.add_argument(
+        "--orientations",
+        required=True,
+        type=str,
+        help="Path to file generated by postprocess.py using output_format orientations.",
+    )
+    io_group.add_argument(
+        "--orientations_sampling",
+        required=False,
+        type=float,
+        default=1.0,
+        help="Factor to map candidate coordinates onto the target. Only relevant if "
+        "target sampling rate differs from candidate orientation sampling rate.",
+    )
+    io_group.add_argument(
+        "-o",
+        "--output_file",
+        required=True,
+        type=str,
+        help="Path to write output H5 file.",
+    )
+
+    alignment_group = parser.add_argument_group("Alignment")
+    alignment_group.add_argument(
+        "--align_orientations",
+        action="store_true",
+        required=False,
+        help="Whether to align extracted orientations based on their angles. Allows "
+        "for efficient subsequent sampling of cone angles.",
+    )
+    alignment_group.add_argument(
+        "--angles_are_vector",
+        action="store_true",
+        required=False,
+        help="Considers euler_z euler_y, euler_x as vector that will be rotated to align "
+        "with the z-axis (1,0,0). Only considered when --align_orientations is set.",
+    )
+    alignment_group.add_argument(
+        "--interpolation_order",
+        dest="interpolation_order",
+        required=False,
+        type=int,
+        default=1,
+        help="Interpolation order for alignment, less than zero is no interpolation.",
+    )
+
+    extraction_group = parser.add_argument_group("Extraction")
+    extraction_group.add_argument(
+        "--box_size",
+        required=False,
+        type=int,
+        help="Box size for extraction, defaults to two times the template.",
+    )
+    extraction_group.add_argument(
+        "--translation_uncertainty",
+        required=False,
+        type=int,
+        help="Sets box size for extraction to template box plus this value.",
+    )
+    extraction_group.add_argument(
+        "--keep_out_of_box",
+        action="store_true",
+        required=False,
+        help="Whether to keep orientations that fall outside the box. If the "
+        "orientations are sensible, it is safe to pass this flag.",
+    )
+
+    args = parser.parse_args()
+
+    return args
+
+
+def main():
+    args = parse_args()
+    orientations = Orientations.from_file(args.orientations)
+    orientations.translations = np.divide(
+        orientations.translations, args.orientations_sampling
+    )
+
+    target = Density.from_file(args.target, use_memmap=True)
+
+    box_size = np.array(args.box_size)
+    box_size = np.repeat(box_size, target.data.ndim // box_size.size).astype(int)
+
+    extraction_shape = np.copy(box_size)
+    if args.align_orientations:
+        extraction_shape[:] = int(np.linalg.norm(box_size) + 1)
+
+    orientations, cand_slices, obs_slices = orientations.get_extraction_slices(
+        target_shape=target.shape,
+        extraction_shape=extraction_shape,
+        drop_out_of_box=not args.keep_out_of_box,
+        return_orientations=True,
+    )
+
+    if args.align_orientations:
+        for index in range(orientations.rotations.shape[0]):
+            rotation_matrix = euler_to_rotationmatrix(orientations.rotations[index])
+            rotation_matrix = np.linalg.inv(rotation_matrix)
+            if args.angles_are_vector:
+                rotation_matrix = rotation_aligning_vectors(
+                    orientations.rotations[index], target_vector=(1, 0, 0)
+                )
+            orientations.rotations[index] = euler_from_rotationmatrix(rotation_matrix)
+
+    filename = generate_tempfile_name()
+    output_dtype = target.data.dtype
+    if args.align_orientations is not None:
+        output_dtype = np.float32
+
+    target.data = target.data.astype(output_dtype)
+
+    dens = Density(
+        np.memmap(
+            filename,
+            mode="w+",
+            shape=(len(obs_slices), *box_size),
+            dtype=output_dtype,
+        ),
+        sampling_rate=(1, *target.sampling_rate),
+        origin=(0, *target.origin),
+    )
+    dens.data[:] = target.metadata["mean"]
+
+    data_subset = np.zeros(extraction_shape, dtype=target.data.dtype)
+    pbar = ProgressBar(message="Aligning ", nchars=80, total=len(obs_slices))
+    for index, (obs_slice, cand_slice) in enumerate(zip(obs_slices, cand_slices)):
+        pbar.update(index + 1)
+
+        data_subset.fill(0)
+        data_subset[cand_slice] = target.data[obs_slice]
+        target_subset = Density(
+            data_subset,
+            sampling_rate=target.sampling_rate,
+            origin=target.origin,
+        )
+
+        if args.align_orientations:
+            rotation_matrix = euler_to_rotationmatrix(orientations.rotations[index])
+            target_subset = target_subset.rigid_transform(
+                rotation_matrix=rotation_matrix,
+                use_geometric_center=True,
+                order=args.interpolation_order,
+            )
+        target_subset.pad(box_size, center=True)
+
+        # target_value = target.data[tuple(orientations.translations[index].astype(int))]
+        # center = np.divide(target_subset.data.shape, 2).astype(int)
+        # print(np.where(target_subset.data == target_value), center)
+        # print(target_subset.data[tuple(center.astype(int))],
+        # target_value,
+        # target_subset.data[tuple(center.astype(int))] == target_value
+        # )
+
+        dens.data[index] = target_subset.data
+    print("")
+
+    target_meta = {
+        k: v for k, v in target.metadata.items() if k in ("mean", "max", "min", "std")
+    }
+    dens.metadata.update(target_meta)
+    dens.metadata["batch_dimension"] = (0,)
+    dens.metadata["normals"] = orientations.rotations
+
+    dens.to_file(args.output_file)
+    orientations.to_file(
+        f"{splitext(args.output_file)[0]}_aligned.tsv", file_format="text"
+    )
+
+if __name__ == "__main__":
+    main()