scipion-em-xmipp 23.3.0.3__py3-none-any.whl → 23.11.0.0__py3-none-any.whl

{scipion_em_xmipp-23.3.0.3.dist-info → scipion_em_xmipp-23.11.0.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scipion-em-xmipp
-Version: 23.3.0.3
+Version: 23.11.0.0
 Summary: Plugin to use Xmipp programs within the Scipion framework (see https://scipion-em.github.io/docs/).
 Home-page: https://github.com/i2pc/scipion-em-xmipp
 Author: I2PC
@@ -8,10 +8,10 @@ Author-email: scipion@cnb.csic.es
 License: UNKNOWN
 Keywords: scipion cryoem imageprocessing scipion-3.0
 Platform: UNKNOWN
-Requires-Dist: scipion-pyworkflow (>=3.0.31)
+Requires-Dist: scipion-pyworkflow >=3.0.31
+Requires-Dist: scikit-learn ==0.22
 Requires-Dist: scipion-em
-Requires-Dist: scikit-learn (==0.22.1)
-Requires-Dist: scipy (<=1.8.1)
+Requires-Dist: scipy <=1.10.0
 Requires-Dist: joblib
 Requires-Dist: peppercorn
 Requires-Dist: plotter

{scipion_em_xmipp-23.3.0.3.dist-info → scipion_em_xmipp-23.11.0.0.dist-info}/RECORD

@@ -1,82 +1,78 @@
-xmipp3/__init__.py,sha256=QwpYzudtRu1ivuszdsF5TdiIYvDC86X6TKyL0_CUxko,13057
+xmipp3/__init__.py,sha256=QuKgvzbrckW-olA05xkWEbz5L9rMOvBFbTj3Nmt2hcg,13311
 xmipp3/base.py,sha256=pFu7FZjm4WeqWbLZJwbmGH3-2YixAIpKyWMFvVrsBYc,21220
-xmipp3/bibtex.py,sha256=0zg0FIpCi59UzLneLc-Wr0tjEX-d2hwSBH1neFG90OQ,26010
+xmipp3/bibtex.py,sha256=YZjuuB_9RC4QOOy5r86cRX3ze2EWz43iGzIDQvtu5HQ,28310
 xmipp3/constants.py,sha256=ND8PUJyUIP3IS3kbq0tZqk77Yq0c4WotRUj_r2gEDxo,3833
 xmipp3/programs.py,sha256=yrMD0EHEq5j_ODCeINbaCp4CEqSgkmioan1O1mAgPY0,11968
-xmipp3/protocols.conf,sha256=rk4lD93Oj7RDc6sVHG2c1fgOvrZmq5f-GKrKlnpjxDc,12552
+xmipp3/protocols.conf,sha256=oyp24nsLnr5TqjLVgPIfJjEwD9QlQ1MCzwuUAj_mlJ0,12386
 xmipp3/utils.py,sha256=JKuEdR40rn6pdm0puwsgzItbNnrFL4sa7pBymVtRzLM,9125
-xmipp3/wizards.py,sha256=De-LT53ip3ZTSBr3DbEQxPPIpXxrvG7q0R3F7u_L3pE,20151
+xmipp3/wizards.py,sha256=kS2ctLuy46m-8XPWrd2705V9Gxbhf4UBa4vKJ8eqius,20343
 xmipp3/xmipp_logo.png,sha256=ggrFNUy5UEBjvKfNvu0T14Kzolnhc-ij9AQ734R27MY,84496
 xmipp3/convert/__init__.py,sha256=y231wRpfDySMgyjLi6xYuO3hTG1NZBNnMRT7dNnYqu8,1211
 xmipp3/convert/convert.py,sha256=89Kay47zY8dguxUrxfrSUkCb__9-qe96h_tQZdzctWc,62027
 xmipp3/convert/dataimport.py,sha256=ssmMLKU1qXDuqjStNJv-zfYNJAJ-0k7EzNyF4jf91IU,13292
-xmipp3/convert/io_coordinates.py,sha256=q8_3KHg_2mC3z8OYBHt8V-2711uFFsbV2NCRKeTSQ9c,1885
-xmipp3/protocols/__init__.py,sha256=6AqDQRw0cdrRSGx3dsnJ-XXSoByOEGmI4R9YTULJJvI,8549
-xmipp3/protocols/protocol_align_volume.py,sha256=BSgl2QWK_vNL_5WdCrQTKYjwj571ovyUe7r7rVeRHcg,18950
-xmipp3/protocols/protocol_align_volume_and_particles.py,sha256=H213YUZfrFeSZW3GwumTBjp-1eMbwlBHc9c2ppnPY-Q,10714
-xmipp3/protocols/protocol_analyze_local_ctf.py,sha256=IfiHD8TGOQT4mogtqJqpVXzcrcfv0Svw-oIJkCEVXh4,7414
+xmipp3/convert/io_coordinates.py,sha256=ZUKEbL7DjJ0jDVJzs2Nnc-sX7QYuAyGSponhP6WYMDI,1963
+xmipp3/protocols/__init__.py,sha256=0O75OJ2F3-ud9FUkMEFnO2M4B8D1F3TVFVO0fXbTwYQ,8554
+xmipp3/protocols/protocol_align_volume.py,sha256=uxFtsb9cB0tz9QkyXvR3pK5457x9sq9F-qyeuOeA2go,19070
+xmipp3/protocols/protocol_align_volume_and_particles.py,sha256=g5dpZfq_iggeTFt2-3iGvc8zFQY_5EaiBg0gycEKPLw,10735
+xmipp3/protocols/protocol_analyze_local_ctf.py,sha256=O1_xWXuKDRGvhhd-BQ1DRMKti_KDqNN_kALzUhvN3DQ,7446
 xmipp3/protocols/protocol_angular_graph_consistency.py,sha256=CjRg1dkOUC8R9EaKKUyypjPSTmPetCkAUQE1Q184gS0,30302
+xmipp3/protocols/protocol_angular_resolution_alignment.py,sha256=EsKm1PfGkkpnzoKuhZqM-e1_99_XVtIBOIGhlgg45qM,8521
 xmipp3/protocols/protocol_apply_alignment.py,sha256=TL89xGiYtPN5mlEhU4R-6yLEzjxIyx2TStiTyXdkvKw,5958
-xmipp3/protocols/protocol_apply_deformation_zernike3d.py,sha256=rlRxaTNmp8X0WBNwBZNF_QTCS38WnUzBtg1M25_aNOo,5673
 xmipp3/protocols/protocol_apply_transformation_matrix.py,sha256=TJJ7IQK_FM_-3488iBCH6JQSnBLBhPg78mYXN2E2PAk,4891
 xmipp3/protocols/protocol_apply_zernike3d.py,sha256=aHb-6oFCLIZV49OXlft_VQgmcO9vd65-g-KFPK-Arbw,10506
 xmipp3/protocols/protocol_assignment_tilt_pair.py,sha256=4bjhPZbffm2jIZV4LLbrw-_fhNbzZVPf1UmzbqhpK_o,10332
 xmipp3/protocols/protocol_break_symmetry.py,sha256=OZvOOsyFMX-pdk69rYo546AxvRZtRFs0GmuT9Vkv6mc,6183
-xmipp3/protocols/protocol_center_particles.py,sha256=V6ePin5uR9NYziKaFGbrKsRh8XG5ZsqdLVS9V9D7sTg,11028
+xmipp3/protocols/protocol_center_particles.py,sha256=2ug42YlvD7PidOLC1EL6U4b-WFm9i6UF8ggn_ksC14E,11159
 xmipp3/protocols/protocol_cl2d.py,sha256=Ksik8xTx2m0DHKDiemOz2q_lhNFOrar6OXMxVrY6a08,27226
 xmipp3/protocols/protocol_cl2d_align.py,sha256=RF_WVqNMnLGXALW5LyIQ43JmoysSyYcrV5vOsnef0oY,8279
 xmipp3/protocols/protocol_classes_2d_mapping.py,sha256=oq6me8X4v4qFJt-GtJ4S1y64qkPCmUVWHkfMgK8XCcA,18032
-xmipp3/protocols/protocol_classification_gpuCorr.py,sha256=oiyTNfVp5GNgQD8hJsUl93N_jiEEvTdWAPhIYWBNKhE,37013
-xmipp3/protocols/protocol_classification_gpuCorr_full.py,sha256=cnRykHISyHmUXLKWLZLBr6rXP5RZQ01loj7PsdWKp0A,40366
-xmipp3/protocols/protocol_classification_gpuCorr_semi.py,sha256=7_i1GX6Ty5upG_deW_C2CgD0MOd_3ZdLxgOC8oxXRuA,18244
-xmipp3/protocols/protocol_classify_kmeans2d.py,sha256=6yZz3o2dooZmo-83vHcT5Pu9Y2p_eA6oKrJuWc7m7D0,12438
 xmipp3/protocols/protocol_compare_angles.py,sha256=NIoQjym4aH3BsMJ7RaMmyswEl9gHkxMnnkQQJdAQaCw,8034
-xmipp3/protocols/protocol_compare_reprojections.py,sha256=gLeW2tE2rXOmMounJmSf5JI4Pa2W-IL6m5Hq9O9biFs,15282
-xmipp3/protocols/protocol_consensus_classes3D.py,sha256=rWp5SyAmw811nzh3mLp2Y-ykLWzilDoabgZOX_r1nE0,31955
-xmipp3/protocols/protocol_consensus_local_ctf.py,sha256=zN6BEyGKtooZMM7_LkC5ZjR52XJ6hFAQMDb0rBZ9IuI,6568
-xmipp3/protocols/protocol_convert_pdb.py,sha256=OCHI8rbHEw8Vhbc1-Ucz30a1YzJ_nLe2FgSCXb-C0Hk,10531
+xmipp3/protocols/protocol_compare_reprojections.py,sha256=nRDA9tvF9wATuNZW7PoQ6H5N9CKDiKnwPeYyxgsG4ug,15333
+xmipp3/protocols/protocol_consensus_classes.py,sha256=En9qEsEpkRqXE0BUOHvJI8b6VTrsZfpgd2x2GTj32eU,24604
+xmipp3/protocols/protocol_consensus_local_ctf.py,sha256=qJrZ1GVJgaNmX60_GvbUDg-qg3FqXnfoLXWhfoXiJss,9953
+xmipp3/protocols/protocol_convert_pdb.py,sha256=S75hJDC43FlODBlCJDzpFS6goKDXeD5Gsl0C7hhm5DM,15268
 xmipp3/protocols/protocol_core_analysis.py,sha256=OHswPqGCEdm8WwvV4tD4aUwa6MxKAGtx3w0CcTGX0ak,9964
-xmipp3/protocols/protocol_create_gallery.py,sha256=KHp1FrseHGMvfy1KRWi6KicYCMYbR4goZAxTcEV-jws,5973
-xmipp3/protocols/protocol_ctf_consensus.py,sha256=iZiUo7jYdZwPxrlVJvd2EFkRWDYOU1qWNA5pvgMCgI4,42641
+xmipp3/protocols/protocol_create_gallery.py,sha256=GwuJxJLkPlxZxUSt-J8oDgPN7wWmFBd4iPENcve_JIY,5970
+xmipp3/protocols/protocol_ctf_consensus.py,sha256=_ug1EQG9COSWK-VHIsMXXDthK4tbRPgt7QUqJyyYrFQ,42582
 xmipp3/protocols/protocol_ctf_correct_wiener2d.py,sha256=thDaon-jYBeXbGM_UiEwfLCeURPwD_7ycgzUzNc3T5g,5819
 xmipp3/protocols/protocol_ctf_defocus_group.py,sha256=c_it4w5tJAxC9HpMzcYp58cZLRXSNS4hjgeJ_L6iKkI,8304
 xmipp3/protocols/protocol_ctf_micrographs.py,sha256=urc8Fk8cA0z6r4FEkzuD2yvQYyGoBv7VZjTlmNBr-A0,28698
+xmipp3/protocols/protocol_deep_center_assignment.py,sha256=87rh6bdYfbOViEn0atEzahwD0ON5Yp4PPBSg-dyCbzk,12691
 xmipp3/protocols/protocol_deep_denoising.py,sha256=z7lkqP8AylC1NMbHkGORUKLAiS9DAffInaZUpbYAAVo,21324
-xmipp3/protocols/protocol_deep_hand.py,sha256=E_ZRO0pvBCRsGTdMW7cpvdzP1ianUmwbuKs3k3-z53Q,7186
-xmipp3/protocols/protocol_deep_micrograph_screen.py,sha256=av-e1O4WyqYe4EGw43XIiKUWAsrDBu0Be2OY7-_3wEc,21735
+xmipp3/protocols/protocol_deep_hand.py,sha256=KeKV6DHqpua1GoL3dWojYhwAHEiUxXy5Mdkr0at77ag,7185
+xmipp3/protocols/protocol_deep_micrograph_screen.py,sha256=AL9c6dqsdSOA1MCEOzYcWd5mtoCfyJyioIXALmJ4Scw,22068
 xmipp3/protocols/protocol_denoise_particles.py,sha256=h6q5xTWfC6UQZE89MqseqNCpf0ufrh3gQeG83gTlemM,7759
 xmipp3/protocols/protocol_eliminate_empty_images.py,sha256=Xil4A_zuprSZ_LjZc79CEKib2-MrUZzxyN5bDLaYaSo,22399
 xmipp3/protocols/protocol_enrich.py,sha256=pymPJpNAHUNtECe89-pdzcVmkdNbVN7kp1PGz9NgwYg,25080
 xmipp3/protocols/protocol_extract_asymmetric_unit.py,sha256=1XOA2waEA0EY8z7iB-2ivJXbiNDegzIyYmkOxTpXseM,8356
-xmipp3/protocols/protocol_extract_particles.py,sha256=iL9JjHZPDknG5GW1sxvdWf1BxQky34WQsWsefw-Epng,23503
-xmipp3/protocols/protocol_extract_particles_movies.py,sha256=xr-1EDWY1-5xM5Gs8Mg5G9VrQPzob5l9tZnEjXCphBo,23258
+xmipp3/protocols/protocol_extract_particles.py,sha256=g-xgiTqibAFozObncZ5ICFmWuivtVpFf-ipVCK7FKUo,26362
+xmipp3/protocols/protocol_extract_particles_movies.py,sha256=DYHNx0RRvcvnEXD6rnEYnp7gbv-hNjtjhKvK47MwpHw,23165
 xmipp3/protocols/protocol_extract_particles_pairs.py,sha256=Cg0I_hptAErRXSrtDZnSrUDMx_P2NFgrFV34pUcQFoM,29349
-xmipp3/protocols/protocol_flexalign.py,sha256=BWEMzc3_gtlmahrkoC8mZ-Lew59LmRUCCDJm14r4IQg,18475
+xmipp3/protocols/protocol_flexalign.py,sha256=FCGlCLc0Rk1HomaFYj9l_DiYPrx1K-7f5DmlzSBhjzI,18498
 xmipp3/protocols/protocol_generate_reprojections.py,sha256=UMVB2e4UnwA44XdiXM9iXjaFIajsD-DHebLt2xfb8-4,9471
 xmipp3/protocols/protocol_helical_parameters.py,sha256=aExrXYis9jmRx4GOagy1TRdTaUeK1nkX3akHSS41aoQ,9841
 xmipp3/protocols/protocol_kerdensom.py,sha256=dwJB8Gs1lynymNjBRVvDbGJpz9p2dRsoTgkT-1B08Fs,12393
-xmipp3/protocols/protocol_kmeans_clustering.py,sha256=VKQ3IRRvKMozBSSWb8dRBmoeGbsKjYgqZmuez1XAEWA,5664
-xmipp3/protocols/protocol_local_ctf.py,sha256=zccUIww_YYMyjVXe-ZnHQ-0sbAUwhk6MQURgDEsilWQ,8077
+xmipp3/protocols/protocol_local_ctf.py,sha256=Kv9vKC6KCt_fgiF5a-4ivKeetFQGMq05jH3vHMTLLFw,8110
 xmipp3/protocols/protocol_metaprotocol_create_subset.py,sha256=Z1dg0H88x00b2W47Ta7qASbDND-zXyDKQnZ2dN2UPw4,3915
 xmipp3/protocols/protocol_metaprotocol_golden_highres.py,sha256=CY0Ny_rURd48Mysxaz4nh6lHNiCnpYFb-UBWk3VFmg4,32782
 xmipp3/protocols/protocol_ml2d.py,sha256=fOkDGOADXgMxT_GeDEf2b7F8W2GdNP8ZFCTM7DEKUxk,17214
-xmipp3/protocols/protocol_movie_gain.py,sha256=Gphlm3woaizjC9AXVrwxLdVS2wv25Q5-VmRdanRBuIA,26961
+xmipp3/protocols/protocol_movie_dose_analysis.py,sha256=PU_I4yDliM-dPytjZ4BaJt1PF956hVvX7uYDpTv99Nc,17827
+xmipp3/protocols/protocol_movie_gain.py,sha256=tc1GU3-VbV1fkxXzPY0nCGMMKO0lEdtt6HCWKR_azKs,24802
 xmipp3/protocols/protocol_movie_max_shift.py,sha256=zrzZAh-mBWNfVJ-2w12EmbaJ7IYBuQOsdqxRzJkebqE,17726
 xmipp3/protocols/protocol_movie_opticalflow.py,sha256=bxZ3Lh8S7_eqXffxZGPjwdRCIy0_4KSyWUazisu2L7o,18030
 xmipp3/protocols/protocol_movie_split_frames.py,sha256=yx4DryyQDyyqLwp0ckyHjy-_aDBMjdvIIBCZ80Xe4OI,7175
 xmipp3/protocols/protocol_multiple_fscs.py,sha256=Q-F-gZIIk8V8jtMB1DW1R2RbDvXloS0USg6Cy1_Wf5c,6491
 xmipp3/protocols/protocol_multireference_alignability.py,sha256=vAcqz_TEpze65PZC8lu3BgQPiudlICwcLObutTD-3ks,27778
 xmipp3/protocols/protocol_normalize_strain.py,sha256=FrhVITNa_9EkZ_BC53uEVjsOKWcpp0EkFlXvBZJSmgQ,3448
-xmipp3/protocols/protocol_particle_boxsize.py,sha256=9Bx2kEgbvO7BSBxSPmJdsw0CnofuG9AZ0ot3JThs5q8,5568
 xmipp3/protocols/protocol_particle_pick.py,sha256=Kk75_SEv12796oOaRL1u80hsNzV1nzFfiOcryAxaT3Y,9784
-xmipp3/protocols/protocol_particle_pick_automatic.py,sha256=3YXtg9ELWfvN8eBCoteGIYytrPzPz1zTdPy1N2oN28w,10978
-xmipp3/protocols/protocol_particle_pick_consensus.py,sha256=uZbj4b_5gEYPKEI-XqiniLfhSH5XiV_jWtdrdwcceWQ,16654
+xmipp3/protocols/protocol_particle_pick_automatic.py,sha256=aIPxwNQ_--uBR00xASG_aijGAY6rIxwLcIpEfFelAL0,11958
+xmipp3/protocols/protocol_particle_pick_consensus.py,sha256=IUf6ya9ixSIdsJl7_wn9RU9tdyUffZjDnvKT70vp55Y,16538
 xmipp3/protocols/protocol_particle_pick_pairs.py,sha256=uAYek--3U5tpFT2d2sTQqj763Zt4CMkt9tuzk3gTMbU,8426
 xmipp3/protocols/protocol_particle_pick_remove_duplicates.py,sha256=MIEnRIHSs_vtbYIouCtBMjsN6N1s1-lqoem18j06jQk,4938
 xmipp3/protocols/protocol_phantom_create.py,sha256=XkZYJODYa1OZFM8WjThMhSAkIm373RFhDc9BK86jHlM,3525
 xmipp3/protocols/protocol_pick_noise.py,sha256=hsZyE9jqdHa5i7VxHHcy04C_uPk29jr1sfI6amtAHXQ,7340
 xmipp3/protocols/protocol_postProcessing_deepPostProcessing.py,sha256=RqcwXuj22BUxJcTprkYqKd7bdyyZUEQUw1J36KslgXA,15158
-xmipp3/protocols/protocol_preprocess_micrographs.py,sha256=TFNSu11VX9sC1lx8MLXuGzNb26Ybk4IYv1nn9WUt4Tk,24220
+xmipp3/protocols/protocol_preprocess_micrographs.py,sha256=eKu-Hdtd8lsxuT1J7JW_N3AJSESkZxL2-HF-iU5E3SM,23961
 xmipp3/protocols/protocol_random_conical_tilt.py,sha256=R5PrC9JGPWylpBrZ70_VPpN5zySPXI6YM6Mdlbpib3Y,17030
 xmipp3/protocols/protocol_ransac.py,sha256=-Ih7qjWcjzKgyUEphVk7bpd9S1fMFaO2AfYalzd2fGk,28957
 xmipp3/protocols/protocol_reconstruct_fourier.py,sha256=bpgjTKv6aphfNmh-VTigXOE49q-eTI_tOtgpw-ZR_dM,10469
@@ -85,34 +81,33 @@ xmipp3/protocols/protocol_reconstruct_significant.py,sha256=VMHCDpc-XKe43jjyPusw
 xmipp3/protocols/protocol_reconstruct_swarm.py,sha256=z_g7HJ6Ix_Ov3zCzLnqkJuPb3vKq82UYCpB87Cles_E,30163
 xmipp3/protocols/protocol_resolution3d.py,sha256=L9e46RaZosxZlfFOi_GCuwNGqxY13LTxrqrwejWiPFE,10241
 xmipp3/protocols/protocol_resolution_bfactor.py,sha256=QKmJO34yfquyDGS5GL_itiwvfelq40eikMujdCaQEfM,7598
-xmipp3/protocols/protocol_resolution_deepres.py,sha256=QHaVgKuCZoPJf2mcOh-22tLXoHhCm67IcCNuaHRoZC4,16477
-xmipp3/protocols/protocol_resolution_directional.py,sha256=sEkqgOtnG6_t-Rovuhi-rF1huDvzoZMdv9huhTg36jM,12893
-xmipp3/protocols/protocol_resolution_fso.py,sha256=V0q3Mz43ggWlf30LUgGH6s120N9J49fdtSCIlDDNRiU,8886
-xmipp3/protocols/protocol_resolution_monogenic_signal.py,sha256=bRJFK10etEP3ztCK8XWssaeECJvbVWYrm2ct3S4sRK4,17148
+xmipp3/protocols/protocol_resolution_deepres.py,sha256=-gbSyzyPRe9HuuVTOZmw5SE0QuqI3dEijnoom61Nn6s,16478
+xmipp3/protocols/protocol_resolution_directional.py,sha256=WcCGzkoiAkwqsnE_538Zoc2mopdjQpFVtFGNy8nLzqU,12894
+xmipp3/protocols/protocol_resolution_fso.py,sha256=bGMw_Y5tFSfPipvV2UfnZOXFpQrfA6qR7CljTXp1XT0,8935
+xmipp3/protocols/protocol_resolution_monogenic_signal.py,sha256=xHOkSmyIKFwS6-PsvhcNpt7qB-P5jQz9iRw3wEkASps,17149
 xmipp3/protocols/protocol_rotate_volume.py,sha256=aL6LM-KByo86g0ByWAp2RqdBRyBBpKvW7mIGtJOSjYo,4337
-xmipp3/protocols/protocol_rotational_spectra.py,sha256=4YvhKhN6RJrKagXQSXVGJsHqquQQU67Qv63Nu5yQnAE,9401
 xmipp3/protocols/protocol_rotational_symmetry.py,sha256=hpBuxzj54aGa283Zr3J18mMGrM1cj-3Wu3ihyh1CsVU,8326
-xmipp3/protocols/protocol_screen_deepConsensus.py,sha256=j3XT-prHRlreXaRUp6nlZiNNwDyZG6SkfwvbRz0Y7yA,88133
+xmipp3/protocols/protocol_screen_deepConsensus.py,sha256=WxE0KfQ87ns1r7V--ILnFzdtWieg_9-1M4lP_a4TMFE,88187
 xmipp3/protocols/protocol_screen_deeplearning.py,sha256=nrhfzoTWPWULTrDDnUD1ELCC_cCrS5-3yaxTBSBsOAY,17530
 xmipp3/protocols/protocol_screen_particles.py,sha256=zg5njvG18d_NCzX3AjRJUXY8FdZmy9K8oqcvmkz2lMg,21002
 xmipp3/protocols/protocol_shift_particles.py,sha256=S4U1W6E73YaneIIibAaD_-1-2tRbDgZgDJQYdpjklyw,8893
 xmipp3/protocols/protocol_shift_volume.py,sha256=iejnfsJkYEJhs9cADX5_r7Iniwnnc8X-nwF4RbU1ADU,5138
-xmipp3/protocols/protocol_simulate_ctf.py,sha256=K7EtVmsVG2IJXPlSh_P6xYDwga5c4Gc-RRlumhw7iVA,5531
+xmipp3/protocols/protocol_simulate_ctf.py,sha256=gvoWmWdao-9kT8mUQGQcx7LSDAGodqIqS7tZ_rm39m0,7117
 xmipp3/protocols/protocol_solid_angles.py,sha256=taET1k3d0v-mUi2fq4cUn8AvWygg7IqMfoGma67Dm5Y,29287
 xmipp3/protocols/protocol_split_volume.py,sha256=4yfrx8BKzMszgZijqJ3iEAHD66DWlVNm4rwWwwsvhTE,5928
-xmipp3/protocols/protocol_split_volume_hierarchical_cluster.py,sha256=2e6fYYz-bJ3i7c15Ds2ucu-m43LYLNZNqCqw-f8ozB4,40429
 xmipp3/protocols/protocol_structure_map.py,sha256=Nf6H_imnkgJTs64-I8FFFtD1CKFmaZ8Sb6ZTD_j33m8,8331
 xmipp3/protocols/protocol_structure_map_zernike3d.py,sha256=EY7rV6vSfyxYXH3ed0FTzNsYu87Ph9klYGqlwuc0eyU,22110
-xmipp3/protocols/protocol_subtract_projection.py,sha256=KJTSvkoIM8A0C-TBAxLbNw4IKcVfkeH7q4gVrmqPAus,12522
-xmipp3/protocols/protocol_tilt_analysis.py,sha256=ZblbkYhsdlrc3v2uBFDYRTCZTNum1LaPkqtkOTOHb6E,28360
-xmipp3/protocols/protocol_trigger_data.py,sha256=TrGfibUdoPEU7jj6wNKPOKgfxQ5mO35RGGUk8hX0KRg,16359
-xmipp3/protocols/protocol_validate_fscq.py,sha256=XXrkFBPoYBUEbQlgMXLhWOEeIiGVBPKQn8ZuecaSzsE,23655
+xmipp3/protocols/protocol_subtract_projection.py,sha256=v1svDU_qGWBu58oGrTVSIB8cJj3INE3Dl97E2DoaXuU,12850
+xmipp3/protocols/protocol_tilt_analysis.py,sha256=q3jaJjflDIvsC13UfERAYQkMokC-eboxvjiTQOVjlT8,27300
+xmipp3/protocols/protocol_trigger_data.py,sha256=8eJiHieg7wHX0Gd7ytyfLHnnyzYMpayVda1v6vFHWvs,15711
+xmipp3/protocols/protocol_validate_fscq.py,sha256=WeRpRgOvalLgRXpGO36Td3YvCJCAkqLGbE739BfIlHQ,23656
 xmipp3/protocols/protocol_validate_nontilt.py,sha256=1XIqu4Inco-Mv-TA6gwas21g1owwagngao05OZLnu54,16415
 xmipp3/protocols/protocol_validate_overfitting.py,sha256=QYKu8Hi6QwbbEsY5V6Riu7K7PWUpj8oS__ZjobjFe80,25116
 xmipp3/protocols/protocol_volume_adjust_sub.py,sha256=HESmNsxutaxtiO0NO7Wgcj7yncGm_o97bgIB6fkblX8,17626
-xmipp3/protocols/protocol_volume_consensus.py,sha256=guIaAMGwj7ge7Q_9D7r3uV-eXTPbIwkGwS2M58oUL14,5595
+xmipp3/protocols/protocol_volume_consensus.py,sha256=miaQo_ldhwAcFefBjIk32iKFpK0SBvaPaVPviD1eoL8,5626
 xmipp3/protocols/protocol_volume_deform_zernike3d.py,sha256=fpZlYE6TRkDkgD4Ozo4RWNCX-ba89bGvqBSn-6Ki8qA,10165
-xmipp3/protocols/protocol_volume_local_sharpening.py,sha256=Gnv0Rw324TUcp96jAv4lEVWH-ae5Y54C3FixzEahPJg,12478
+xmipp3/protocols/protocol_volume_local_adjust.py,sha256=bhCJbMYiSXxDbfE2e-GBr19HUYHYnfKCuAej8ANoG64,5980
+xmipp3/protocols/protocol_volume_local_sharpening.py,sha256=iFjA4DKEIVKVE1ekNfbCrMWeTRBQwIjXJIQu7DwbP24,12479
 xmipp3/protocols/protocol_volume_strain.py,sha256=OQU0mLlHBK0add_gP9hWwDc19FxGAYY4XmjRkKfcB3M,6777
 xmipp3/protocols/protocol_write_testC.py,sha256=LfUhtQeT_lsZjw7yHDa0B-m33V-UmfJYMn_fFyruPnc,3288
 xmipp3/protocols/protocol_write_testP.py,sha256=2CaljDnQFTCIq7Jg6OdQjJmWHOOGpLPgdvyaN2E6cbs,4485
@@ -120,14 +115,14 @@ xmipp3/protocols/protocol_preprocess/__init__.py,sha256=pcMVGV30RoFawgvIE1JtD90_
 xmipp3/protocols/protocol_preprocess/geometrical_mask.py,sha256=8ZFzffgXlSsth83X_xOBYcFhccZgEKhVsAJhjo7AHpA,15938
 xmipp3/protocols/protocol_preprocess/protocol_add_noise.py,sha256=3gufSX9E5jsL1NgonGuVQH_DJa4-o9pynD6vbr0uuw4,12166
 xmipp3/protocols/protocol_preprocess/protocol_create_mask2d.py,sha256=EHPUzM-iDX7ETUxAE4VSrc2Rq9Isl6dgl7teZQva4CY,4237
-xmipp3/protocols/protocol_preprocess/protocol_create_mask3d.py,sha256=jM-gzxGG4L90CwPuNkimrOzL-0WU1G0-tw1MTp5wJqU,18575
-xmipp3/protocols/protocol_preprocess/protocol_crop_resize.py,sha256=DWrd_MigmWGZvXJM7KSsNhbPrZAnWjTsnmUQbnEv9fk,23009
-xmipp3/protocols/protocol_preprocess/protocol_filter.py,sha256=obIGVFbp71l38ftAFFRBMGT0swTtttyOBjvnm0dSwME,22928
+xmipp3/protocols/protocol_preprocess/protocol_create_mask3d.py,sha256=EkEzJJZTBwmMRa5j5jYy22gbIvOESyjGSkxPHgk7Atc,18818
+xmipp3/protocols/protocol_preprocess/protocol_crop_resize.py,sha256=3_T2DPQgbx5VK-zF4mpeBA1TbpY-CiE3fkLEyhUWX0g,25596
+xmipp3/protocols/protocol_preprocess/protocol_filter.py,sha256=NNeZ7A_co3h03jh0LdEPmpdMXozfESF_AdJuDJ2rWNI,23056
 xmipp3/protocols/protocol_preprocess/protocol_image_operate.py,sha256=xKizCA9cxas0dWOd_DQEVMKNGyRC5Rzr7B2ml-Uufo0,16881
 xmipp3/protocols/protocol_preprocess/protocol_mask.py,sha256=5O_wN4ifd1vY1on25J6H5Xj6L0eyV4fcr-u1rBqw4Ys,11716
-xmipp3/protocols/protocol_preprocess/protocol_movie_resize.py,sha256=oGHODoNOtNl1uvKDJfNMQwDfrjqz-NSnOVGB32pPMPA,10822
-xmipp3/protocols/protocol_preprocess/protocol_preprocess.py,sha256=Wm9PjJ9zWnFScmYPIt615THUFSBHZsbetc_Fc3-HRls,39852
-xmipp3/protocols/protocol_preprocess/protocol_process.py,sha256=THgrDVHDRH7l5r2VO4vhtfEkUvl-XEzs2qR9TYzU2Y4,7949
+xmipp3/protocols/protocol_preprocess/protocol_movie_resize.py,sha256=WfaQljG1c9UZXd-gaWRdQXeZEplLYZGWxYiuGopaqto,10942
+xmipp3/protocols/protocol_preprocess/protocol_preprocess.py,sha256=ZJjSeR2Lei4_WUMN94vN7d4RmoXjhSSFLjSZMSG4euU,39938
+xmipp3/protocols/protocol_preprocess/protocol_process.py,sha256=NpwdL7FGamwqcfGG6UbG0OqvBhjruRx5Pd4L_bnJ3yc,8025
 xmipp3/protocols/protocol_projmatch/__init__.py,sha256=fDxNicNXSbBa3WsuFouhk3INxsdQ7mlBhEYNaypFZXw,1278
 xmipp3/protocols/protocol_projmatch/projmatch_form.py,sha256=T6qmARWQoYUbKBiw-pCTOYnoHIOpuf-qyfXVHoBzx9o,36535
 xmipp3/protocols/protocol_projmatch/projmatch_initialize.py,sha256=poaVKWbyt2Bl38XHr9qOCCCRZANALnNzAhbazXgWWz4,10650
@@ -140,6 +135,7 @@ xmipp3/tests/test_protocol_apply_transformation_matrix.py,sha256=oviulcS710BpL1_
 xmipp3/tests/test_protocol_compare_angles.py,sha256=wBldiS1_LJVHfdg4g8LMDfWORR4l5adZsZkj661SgNg,5361
 xmipp3/tests/test_protocol_consensus_classes3D.py,sha256=HLz1X9LuZDRTwhjDI6gqk72qm4Yguxc76BZL_wnxgKw,11006
 xmipp3/tests/test_protocol_ctf_consensus.py,sha256=EtYxHmrHLY1illmjFMNPQJzVhGNgzcbcksr6-NaHA04,9120
+xmipp3/tests/test_protocol_deep_center_assignment.py,sha256=DxzLeyBejdzInV-TsyX2VCkRIVfF1u-80TnvITe3750,5607
 xmipp3/tests/test_protocol_deep_denoising.py,sha256=kgqmGy-kBhkskCkjk-FMFTPf0hCrzKDdS8JKKIiGlyE,2815
 xmipp3/tests/test_protocol_extract_asymmetric_unit.py,sha256=Ya8zy3wuKi10r-_LVwpavYgzVrGy-5M3Gy05MHNmr7M,23298
 xmipp3/tests/test_protocol_monodir.py,sha256=nt-5KEzbVAtsNeQ9OOifYSp1kN2N7tZwxtwS1ipbljY,3741
@@ -147,62 +143,61 @@ xmipp3/tests/test_protocol_multiple_fsc.py,sha256=E7rhBJI9qJXAnbuxARK9auwnMxmYtI
 xmipp3/tests/test_protocol_multireference_alignability.py,sha256=IV-INSzOnwS7avyHWp4kvCr7xkaF_BFrX08YCfwvie0,5825
 xmipp3/tests/test_protocol_reconstruct_fourier.py,sha256=pMkRLLWQaFgaGwA55niU_dKEHDZzjHEcUIXbFHDPuGs,3533
 xmipp3/tests/test_protocol_screen_deepConsensus.py,sha256=r-qNtYkJ5EAVltUZ38mwN_MlEO8ZeqXWCumAbZFMJz8,8003
-xmipp3/tests/test_protocol_simulate_ctf.py,sha256=G7wwmkkg4PTTxjQykxx9-AMLtaztXDMHkkpgM40-J7U,4749
+xmipp3/tests/test_protocol_simulate_ctf.py,sha256=G1PImqwh0ZEOfpl6RK6xeUqJmWIE2JWQxuSaF0eWmVg,7484
 xmipp3/tests/test_protocol_validate_fscq.py,sha256=RL8UTe8tgn_IU8mazmuiQzfFQjmoJkZHxi-96rtDInI,2699
 xmipp3/tests/test_protocol_validate_overfitting.py,sha256=PSFRoARteTABLZxJ4ZuWJUnh34QT2JQ6gekqOTgpG6w,3598
 xmipp3/tests/test_protocols_add_noise.py,sha256=Uc6Kc5KaxXUeX6GedbHV3h7svSQoPrXfbHsqc6J6BQk,5209
-xmipp3/tests/test_protocols_continuousflex.py,sha256=leaWrfmCMkMO2lnzdS2Pz-YHf02WK6ElB6E_eRB8rbs,5649
+xmipp3/tests/test_protocols_angular_resolution_alignment.py,sha256=pVhSBXI4vs025a0LYI8sogFDWPz9uOlC5wuLpqcViBE,3874
+xmipp3/tests/test_protocols_continuousflex.py,sha256=y_WeCm-XiZ5rJS1lx4i0TsGoWNf3TeHwL3RC7vVr_Q4,6940
 xmipp3/tests/test_protocols_deepVolPostprocessing.py,sha256=ZUSkLaR2sRlvZoaWPYwIUmDBC0X5DRy7peRd8EieseY,7143
 xmipp3/tests/test_protocols_deepres.py,sha256=rXc-kAWZ8gGGS7L8e27P-ZPsFo5BPyqZKFl25V7dWII,3635
 xmipp3/tests/test_protocols_fso.py,sha256=CrVAVoBD9UbLVKT21TB0Q-tVnZ7qEsm4zcELzDnN3CU,4274
-xmipp3/tests/test_protocols_gpuCorr_classifier.py,sha256=Pkwri9EnsB9EVf07cVB-eq3KZOSAP_MxiugFbBsYQwI,6328
-xmipp3/tests/test_protocols_gpuCorr_fullStreaming.py,sha256=_-yfg9T3mTV8zwJyaskHhZHGhnGS9-rBq8c5U7yT4zI,6709
-xmipp3/tests/test_protocols_gpuCorr_semiStreaming.py,sha256=4yW9l1o6VwOFk4wO6dOJjAUytFka5YdGhnhJv6Qrldk,2836
 xmipp3/tests/test_protocols_highres.py,sha256=cDvRxn6JUI1WQhXjT-83u32hOETBDxt-F5F_ZFx0wJI,4411
-xmipp3/tests/test_protocols_local_defocus.py,sha256=OD-vP5_3IU0t8_gSYm-Sc2F0vDaCa5xjMBe70Xkd0JI,8885
+xmipp3/tests/test_protocols_local_defocus.py,sha256=XGXZTas0pqhHkKfZEky7a8sqLC14rB8KqoOPD27pzZE,9067
 xmipp3/tests/test_protocols_localdeblur.py,sha256=iKf-CFwts-0yePzuztB8czbQLSYvpxHv2gT89I0RHXc,7300
 xmipp3/tests/test_protocols_metaprotocol_golden_highres.py,sha256=T5H6NuzvFIBFTj7y3Pq5OfkNMrrTmqK5KxSoHLyEJIY,4034
-xmipp3/tests/test_protocols_mixed_movies.py,sha256=hv5aiKxb6-E9xPE4DT7vMcTWRCr88vNWHIXw8WQTrsg,7293
+xmipp3/tests/test_protocols_mixed_movies.py,sha256=kAAqNx33TMoOH0v6TaTyfUvdSAQ-vEtUalf6ecgepsM,6151
 xmipp3/tests/test_protocols_monores.py,sha256=FlLhcGUIGrErRh7KKCHo48dB-zrE0i9btLQxTOb-g3U,5023
 xmipp3/tests/test_protocols_realignment_classes.py,sha256=SrMOjTRr46iN69Prhpvyh9kU7VjnxhSCn3FAdBFni9U,6399
 xmipp3/tests/test_protocols_solid_angles.py,sha256=vJ5hrZqRYfPrp9bP9SYLDqzVO__kL6AjAOBJOeajJR0,6985
-xmipp3/tests/test_protocols_xmipp_2d.py,sha256=qw-1OGfxy7cbOfud3VolYm3igJWfBazmqaFT_P5Wp7Y,76668
-xmipp3/tests/test_protocols_xmipp_3d.py,sha256=L2auaTkVAkYN0Z_BGnSfHdMwtrbc6M0XhwXZ8_2DSuc,161922
-xmipp3/tests/test_protocols_xmipp_mics.py,sha256=qTJSPupcEEC5ZyOK_ar0bYHNMr-2VGflPbqtkXMa7Nw,61131
+xmipp3/tests/test_protocols_xmipp_2d.py,sha256=rl9QrVth3-VnXfxAYq-nYdYdgLcP_hy8Kmv5iLz_jcw,75260
+xmipp3/tests/test_protocols_xmipp_3d.py,sha256=dyKNJr0H9_6TSUwSpz699PLcvN6vZV5NHsENSFv6Qrw,169580
+xmipp3/tests/test_protocols_xmipp_mics.py,sha256=NV0ffSbX0W5f_6fL9ueOPUL1mVEA1caJYeB8KUKX-gQ,59879
 xmipp3/tests/test_protocols_xmipp_movie_resize.py,sha256=XR1gYYZeDhNOkDkZhimPDbqcYwss5z-zbhJ73ZM0a5g,6494
-xmipp3/tests/test_protocols_xmipp_movies.py,sha256=Rk9_tSQpI_SWzPTlqh13z507RGpstfviFeaXhrLY9YM,35140
+xmipp3/tests/test_protocols_xmipp_movies.py,sha256=SFn8sZyFl3ROatSWCl4CmhKA1nAkygJDNQFgFe0r2sY,38274
 xmipp3/tests/test_protocols_zernike3d.py,sha256=bTXCK4wBKSJZK1KCZXec3j8y1mVLoBxE5bF3AGbOsNs,18132
-xmipp3/viewers/__init__.py,sha256=Gh3tEsRyFsEaGqQUZDWWCf_iGZe88H7aJupq2AVNEws,3533
+xmipp3/viewers/__init__.py,sha256=gHkUPN2FOp-vvoLRcZzoHjatMNdmBTWp6607pnjaQsI,3618
 xmipp3/viewers/plotter.py,sha256=YHDqAs7_rbv8cXMmwmg42YeeBnesdX44awrppX3VJw0,3875
-xmipp3/viewers/viewer.py,sha256=yLV38PsBItMwYJBJ_de1MABqYJykyC-k1u0l6eND0Qw,21483
+xmipp3/viewers/viewer.py,sha256=D_elkqLkG5a0M82RfuoJj2Zn1TuDN9Uyaf0PcV64GY0,19688
 xmipp3/viewers/viewer_analyze_local_ctf.py,sha256=-Oa7flu05KxP8M6AlZRaWKCRqZljRz23Z6Ncz1qDHhw,4866
+xmipp3/viewers/viewer_angular_resolution_alignment.py,sha256=9DCZ94TAedHltvlKf99BEFtgFuoMisKipMwubPn82lU,5155
 xmipp3/viewers/viewer_cl2d.py,sha256=7uBU6zYOkhYqjMNWFUPFbMOPsqWja9DaTssp_ju6AXw,8764
-xmipp3/viewers/viewer_classes3D.py,sha256=2hwffWko63m-37atTdq7VQCMQu7KyLHEB9qdfWIbeto,6564
-xmipp3/viewers/viewer_consensus_classes3D.py,sha256=qbqSrDRkWTTQj6z6lq1sC3mTfa2K4ewruhznekgAhZQ,12919
+xmipp3/viewers/viewer_consensus_classes.py,sha256=En4EW8tYDS0NLmGoM9IBz_KM9PoBtDo-AqfVxmUDFeE,5434
 xmipp3/viewers/viewer_ctf_consensus.py,sha256=gosd9D2iuTUHgdlQlHIGS_HBybThR1S8SBfgM096e_8,7669
 xmipp3/viewers/viewer_deepEMHancer.py,sha256=ok5e2NfPeK8Joa0Y7Wp0GQG00Pk7AAG19xOE42A1l6c,5741
 xmipp3/viewers/viewer_deep_consensus.py,sha256=ohwXSMb-C4EZh7fNw3JVfxYxTzCVzyDLEPoeC4yqLHg,5608
 xmipp3/viewers/viewer_deep_micrograph_cleaner.py,sha256=gFHOPirTM6-i9bHxCs9Fbkh4GQ9fxc7FINDNib0jkdA,5694
+xmipp3/viewers/viewer_dose_analysis.py,sha256=9u5WNvJfa3sTOT1enigF5zZYtyzQM2j5uTG6Dn8ybEY,4949
 xmipp3/viewers/viewer_eliminate_empty_images.py,sha256=LMDYe4iql1kFOESBbwyClzNezizYKv9a8LHtvlPCboM,7278
 xmipp3/viewers/viewer_extract_asymmetric_unit.py,sha256=ljuDD9JcTSnfI9Ha9KJK8M62NqzwzPAm1RGnUuyhcdA,7163
 xmipp3/viewers/viewer_local_sharpening.py,sha256=_j_4RZISQjWzrBFmsI88DrNqxbT3Ng1AJRmo0MfdCCk,4408
-xmipp3/viewers/viewer_metaprotocol_golden_highres.py,sha256=2G0VkH5GlOH7iLGMNKi3W8H_PFFEp_H18lDH1Y8xSCQ,5495
+xmipp3/viewers/viewer_metaprotocol_golden_highres.py,sha256=PwfPMwTo4z_4Fzc-fBV7VLf4RswvMwoF9vlAqd1o9uI,5373
 xmipp3/viewers/viewer_ml2d.py,sha256=XL1NL8mg-W8TC0fHemD-eR9mHxgUMBnF2d9gwJagC7s,8451
 xmipp3/viewers/viewer_movie_alignment.py,sha256=TiCqybpFc1TOhuZeXzQ-YbS8pnOmXplm5XIwaDQG_nE,5368
 xmipp3/viewers/viewer_normalize_strain.py,sha256=L54CZvxaU9ezu223jgvOSTBn4yYWs2x9q87_3vvHi9k,2804
 xmipp3/viewers/viewer_pdb_deform_zernike3d.py,sha256=g5-ntcOt7841rFFGPRb6NK-wQ2FfbBz2P1E980uENZo,4653
-xmipp3/viewers/viewer_projmatch.py,sha256=kqZ3Ubq8DaYpzElk-9KRksQeZdH7JRk23taFKjM2EIo,37770
+xmipp3/viewers/viewer_projmatch.py,sha256=oSBQO8ffVPF8Mixaj4zvcIcadlrau6Z1DU6qFGyos-g,37634
 xmipp3/viewers/viewer_ransac.py,sha256=hfjj3ySF2hlSIicw6WTezZhau9aaQJNGKYR6nP8VYrE,2445
 xmipp3/viewers/viewer_reconstruct_highres.py,sha256=bDcxUyGU4wlRFdBnfbhMiCLRB8b_C8LqaKkXgX0lg00,13184
 xmipp3/viewers/viewer_resolution3d.py,sha256=AfKbCxLzuJG3pJQLPxNgK86WRSWXrgRSEDNjzbM5Y6E,14152
 xmipp3/viewers/viewer_resolution_bfactor.py,sha256=iknAViynFLy3Sx4fs2DvR9zpLUcxTKCyS9VkhMHb1Vw,4933
 xmipp3/viewers/viewer_resolution_deepres.py,sha256=M1X9wW7V4yU0BaMxezFNSHhfd4Rpj34ruc-tAnO1T5k,8632
-xmipp3/viewers/viewer_resolution_directional.py,sha256=EuMHZqe-Jz5LKkxt5cRe4Gd4WR8-IoUFbQjFBIUnWFA,20319
-xmipp3/viewers/viewer_resolution_fso.py,sha256=hzqX-409e6OcOz23DyzfHTviEF9q4KDBreXnPyGIZ_I,15761
-xmipp3/viewers/viewer_resolution_monogenic_signal.py,sha256=-fbq6PulPCOdUAc4G7pTJvroqLzB8H0XJxaK4vutv5M,10952
+xmipp3/viewers/viewer_resolution_directional.py,sha256=SOnybW40HuMglekNnD-YGF2ZPMXLZuGf-AwmvRUNg98,20322
+xmipp3/viewers/viewer_resolution_fso.py,sha256=WIbsYmTKnuJ-wVLAgMoXHmrMMkrb6ukfboyz2NHDUtc,15874
+xmipp3/viewers/viewer_resolution_monogenic_signal.py,sha256=GCrWKLb9IFVcGY8zKzCNnXWy15T_jPPhM2uZjJ0un8c,11088
 xmipp3/viewers/viewer_solid_angles.py,sha256=S2QANz-8VdoK_8kKTYtkhI6SkPQyRuiPkMaz2bQJCIY,3970
 xmipp3/viewers/viewer_split_volume.py,sha256=4rmH0ixpNS1eR_FLgmD5lgo4IUmqTPNST7_-wLMHkj4,2146
-xmipp3/viewers/viewer_structure_map.py,sha256=OBuMgFX3sUJg8dSnsC2xop_dJstv7768pq6DherAw_w,14398
+xmipp3/viewers/viewer_structure_map.py,sha256=qCD-kxulB7nR_Oiha9AkkHwOfHqcuPpkW4aqIjVHxLo,14534
 xmipp3/viewers/viewer_subtract_projection.py,sha256=UPm_G_CwTUgtgzVMtNCF3NFgnfwxJSy3HmaKYW2WECE,2860
 xmipp3/viewers/viewer_swarm.py,sha256=liXSpVMNqO0YzcexF6hyl8n8V6j2t7yB8D42dHWIazk,2590
 xmipp3/viewers/viewer_validate_fscq.py,sha256=suGL5IqAv6Nsvs9oNscFcpD_zbienRMdQ7Mns2u3m58,18651
@@ -212,9 +207,9 @@ xmipp3/viewers/viewer_volume_consensus.py,sha256=S7YViiZ9w5xAGhfyj1RnDypVWsQ7PKh
 xmipp3/viewers/viewer_volume_deform_zernike3d.py,sha256=BOeI7go5w2RRwGjV9kPm2U76tVJRaHww1Pl0zUCXQRw,8903
 xmipp3/viewers/viewer_volume_strain.py,sha256=4LQUrceVMB6OaAfTpFXdn3vGv-sXQzUIPDEPELYfasY,2378
 xmipp3/viewers/viewer_volume_subtraction.py,sha256=3RbwJQIaCcdzldrFODLgWlFbCips1450RDVzngLRRoU,5121
-scipion_em_xmipp-23.3.0.3.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-scipion_em_xmipp-23.3.0.3.dist-info/METADATA,sha256=3VFtUBL-37wwbwC5BCrFCuID1LRUJbMmaIwAHtSwchQ,1628
-scipion_em_xmipp-23.3.0.3.dist-info/WHEEL,sha256=pkctZYzUS4AYVn6dJ-7367OJZivF2e8RA9b_ZBjif18,92
-scipion_em_xmipp-23.3.0.3.dist-info/entry_points.txt,sha256=uAfbaIdLcZ7JWL0tWzQVwsVEyyOZb1WcBX4YZMqRrIk,37
-scipion_em_xmipp-23.3.0.3.dist-info/top_level.txt,sha256=qnLFoZzwKticb33xgeSAJv3P7nD2nHMTFKYzxAorOOQ,7
-scipion_em_xmipp-23.3.0.3.dist-info/RECORD,,
+scipion_em_xmipp-23.11.0.0.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+scipion_em_xmipp-23.11.0.0.dist-info/METADATA,sha256=IULZhDq6q8pFJVatS-j-3hu2eKIPhGyOhB1B4jk7PSg,1622
+scipion_em_xmipp-23.11.0.0.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+scipion_em_xmipp-23.11.0.0.dist-info/entry_points.txt,sha256=uAfbaIdLcZ7JWL0tWzQVwsVEyyOZb1WcBX4YZMqRrIk,37
+scipion_em_xmipp-23.11.0.0.dist-info/top_level.txt,sha256=qnLFoZzwKticb33xgeSAJv3P7nD2nHMTFKYzxAorOOQ,7
+scipion_em_xmipp-23.11.0.0.dist-info/RECORD,,

{scipion_em_xmipp-23.3.0.3.dist-info → scipion_em_xmipp-23.11.0.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.40.0)
+Generator: bdist_wheel (0.42.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

xmipp3/__init__.py

@@ -37,12 +37,15 @@ import pyworkflow.utils as pwutils
 from .base import *
 from .constants import XMIPP_HOME, XMIPP_URL, XMIPP_DLTK_NAME
 
-_logo = "xmipp_logo.png"
-_references = ['delaRosaTrevin2013', 'Sorzano2013']
-_currentBinVersion = '3.23.03.0'
-# This will allow scipion to detect the plugin version and print it in the log.
-__version__ = _currentBinVersion[2:] + ".3"  # Set this to ".0" on each xmipp binary release, otherwise increase it --> ".1", ".2", ...
+type_of_version = 'release' #'devel'
+_logo = "xmipp_logo" + ("" if type_of_version == 'release' else '_devel') + '.png'
 
+_references = ['delaRosaTrevin2013', 'Sorzano2013', 'Strelak2021']
+_currentBinVersion = '3.23.11.0'
+__version__ = _currentBinVersion[2:] + ".0"  # Set this to ".0" on each xmipp binary release, otherwise increase it --> ".1", ".2", ...
+
+# Requirement version variables
+NVIDIA_DRIVERS_MINIMUM_VERSION = 450
 
 class Plugin(pwem.Plugin):
     _homeVar = XMIPP_HOME
@@ -209,38 +212,37 @@ def installDeepLearningToolkit(plugin, env):
                                                env=plugin.getEnviron(),
                                                stdout=subprocess.PIPE
                                                ).stdout.read().decode('utf-8').split(".")[0]
-            try:
-                int(nvidiaDriverVer)
-            except ValueError:
-                nvidiaDriverVer = None
-            if int(nvidiaDriverVer) < 390:
+            if int(nvidiaDriverVer) < NVIDIA_DRIVERS_MINIMUM_VERSION:
                 preMsgs.append("Incompatible driver %s" % nvidiaDriverVer)
-                cudaMsgs.append("Your NVIDIA drivers are too old (<390). "
+                cudaMsgs.append(f"Your NVIDIA drivers are too old (<{NVIDIA_DRIVERS_MINIMUM_VERSION}). "
                                 "Tensorflow was installed without GPU support. "
-                                "Just CPU computations enabled (slow computations).")
+                                "Just CPU computations enabled (slow computations)."
+                                f"To enable CUDA (drivers>{NVIDIA_DRIVERS_MINIMUM_VERSION} needed), "
+                                "set CUDA=True in 'scipion.conf' file")
                 nvidiaDriverVer = None
-        except Exception as e:
-            preMsgs.append(str(e))
+        except (ValueError, TypeError):
+            nvidiaDriverVer = None
+            preMsgs.append("Not nvidia driver found. Type: "
+                           " nvidia-smi --query-gpu=driver_version --format=csv,noheader")
+            preMsgs.append(
+                "CUDA will NOT be USED. (not found or incompatible)")
+            msg = ("Tensorflow installed without GPU. Just CPU computations "
+                   "enabled (slow computations).")
+            cudaMsgs.append(msg)
+            useGpu = False
 
     if nvidiaDriverVer is not None:
-        preMsgs.append("CUDA support find. Driver version: %s" % nvidiaDriverVer)
-        msg = "Tensorflow installed with CUDA SUPPORT."
+        preMsgs.append("CUDA support found. Driver version: %s" % nvidiaDriverVer)
+        msg = "Tensorflow will be installed with CUDA SUPPORT."
         cudaMsgs.append(msg)
         useGpu = True
-    else:
-        preMsgs.append("CUDA will NOT be USED. (not found or incompatible)")
-        msg = ("Tensorflow installed without GPU. Just CPU computations "
-               "enabled (slow computations). To enable CUDA (drivers>390 needed), "
-               "set CUDA=True in 'scipion.conf' file")
-        cudaMsgs.append(msg)
-        useGpu = False
+
 
     # commands  = [(command, target), (cmd, tgt), ...]
-    cmdsInstall = [(cmd, envName + ".yml") for cmd, envName in
-                   CondaEnvManager.yieldInstallAllCmds(useGpu=useGpu)]
+    cmdsInstall = list(CondaEnvManager.yieldInstallAllCmds(useGpu=useGpu))
 
     now = datetime.now()
-    installDLvars = {'modelsUrl': "http://scipion.cnb.csic.es/downloads/scipion/software/em",
+    installDLvars = {'modelsUrl': "https://scipion.cnb.csic.es/downloads/scipion/software/em",
                      'syncBin': plugin.getHome('bin/xmipp_sync_data'),
                      'modelsDir': plugin.getHome('models'),
                      'modelsPrefix': "models_UPDATED_on",
@@ -267,6 +269,6 @@ def installDeepLearningToolkit(plugin, env):
                          " fi" % installDLvars,           # End of command
                          installDLvars['xmippLibToken'])  # Target
 
-    env.addPackage(XMIPP_DLTK_NAME, version='0.2', urlSuffix='external',
+    env.addPackage(XMIPP_DLTK_NAME, version='1.0', urlSuffix='external',
                    commands=[xmippInstallCheck]+cmdsInstall+[modelsDownloadCmd],
                    deps=[], tar=XMIPP_DLTK_NAME+'.tgz')

xmipp3/bibtex.py

@@ -604,5 +604,59 @@ url = {https://www.sciencedirect.com/science/article/pii/S104784772100085X},
 author = {E. Fernández-Giménez and M. Martínez and R. Sánchez-García and R. Marabini and E. Ramírez-Aportela and
 P. Conesa and J.M. Carazo and C.O.S. Sorzano},
 }
+
+@Article{Strelak2021,
+AUTHOR = {Strelak, David and Jiménez-Moreno, Amaya and Vilas, José L. and Ramírez-Aportela, Erney and Sánchez-García, Ruben and Maluenda, David and Vargas, Javier and Herreros, David and Fernández-Giménez, Estrella and de Isidro-Gómez, Federico P. and Horacek, Jan and Myska, David and Horacek, Martin and Conesa, Pablo and Fonseca-Reyna, Yunior C. and Jiménez, Jorge and Martínez, Marta and Harastani, Mohamad and Jonić, Slavica and Filipovic, Jiri and Marabini, Roberto and Carazo, José M. and Sorzano, Carlos O. S.},
+TITLE = {Advances in Xmipp for Cryo–Electron Microscopy: From Xmipp to Scipion},
+JOURNAL = {Molecules},
+VOLUME = {26},
+YEAR = {2021},
+NUMBER = {20},
+ARTICLE-NUMBER = {6224},
+URL = {https://www.mdpi.com/1420-3049/26/20/6224},
+PubMedID = {34684805},
+ISSN = {1420-3049},
+DOI = {https://doi.org/10.3390/molecules26206224}
+}
+
+
+@article{Fernandez-Gimenez2023a,
+title = {A new algorithm for particle weighted subtraction to eliminate signals from unwanted components in Single Particle Analysis},
+journal = {Journal of Structural Biology},
+volume = {215},
+number = {4},
+year = {2023},
+issn = {1047-8477},
+doi = {https://doi.org/10.1016/j.jsb.2023.108024},
+url = {https://www.sciencedirect.com/science/article/pii/S1047847723000874},
+author = {E. Fernández-Giménez, M. Martínez, R. Marabini, D. Strelak, R. Sánchez-García, J.M. Carazo and C.O.S. Sorzano},
+}
+
+@article{Fernandez-Gimenez2023b,
+title = {Local defocus estimation in Single Particle Analysis in Cryo-Electron Microscopy},
+journal = {Journal of Structural Biology},
+volume = {215},
+number = {4},
+year = {2023},
+issn = {1047-8477},
+doi = {https://doi.org/10.1016/j.jsb.2023.108030},
+url = {https://www.sciencedirect.com/science/article/pii/S104784772300093X},
+author = {E. Fernández-Giménez, J.M. Carazo and C.O.S. Sorzano},
+
+
+@Article{Strelak2023performance,
+AUTHOR = {Střelák, David and Marchán, Daniel and Carazo, José María and S. Sorzano, Carlos O.},
+TITLE = {Performance and Quality Comparison of Movie Alignment Software for Cryogenic Electron Microscopy},
+JOURNAL = {Micromachines},
+VOLUME = {14},
+YEAR = {2023},
+NUMBER = {10},
+ARTICLE-NUMBER = {1835},
+URL = {https://www.mdpi.com/2072-666X/14/10/1835},
+ISSN = {2072-666X},
+DOI = {https://doi.org/10.3390/mi14101835}
+
+}
+
 """
 

xmipp3/convert/io_coordinates.py

@@ -17,9 +17,10 @@ def readSetOfCoordsFromPosFnames(posDir, setOfInputCoords, sqliteOutName,
     """
 
     inputMics = setOfInputCoords.getMicrographs()
+    inputMicsPointer = setOfInputCoords.getMicrographs(asPointer=True)
     cleanPath(sqliteOutName)
     setOfOutputCoordinates= SetOfCoordinates(filename= sqliteOutName)
-    setOfOutputCoordinates.setMicrographs(inputMics)
+    setOfOutputCoordinates.setMicrographs(inputMicsPointer)
     setOfOutputCoordinates.setBoxSize(setOfInputCoords.getBoxSize())
     readSetOfCoordinates(posDir, micSet=inputMics,
                            coordSet=setOfOutputCoordinates,

xmipp3/protocols/__init__.py

@@ -31,6 +31,7 @@ from .protocol_preprocess import *
 from .protocol_assignment_tilt_pair import XmippProtAssignmentTiltPair
 from .protocol_align_volume import XmippProtAlignVolume, XmippProtAlignVolumeForWeb
 from .protocol_angular_graph_consistency import XmippProtAngularGraphConsistency
+from .protocol_angular_resolution_alignment import XmippProtResolutionAlignment
 from .protocol_preprocess.protocol_add_noise import (XmippProtAddNoiseVolumes,
                                                      XmippProtAddNoiseParticles)
 from .protocol_apply_alignment import XmippProtApplyAlignment
@@ -38,10 +39,7 @@ from .protocol_apply_transformation_matrix import XmippProtApplyTransformationMa
 from .protocol_break_symmetry import XmippProtAngBreakSymmetry
 from .protocol_cl2d_align import XmippProtCL2DAlign
 from .protocol_cl2d import XmippProtCL2D
-from .protocol_classify_kmeans2d import XmippProtKmeansClassif2D
-from .protocol_classification_gpuCorr import XmippProtGpuCrrCL2D
-from .protocol_classification_gpuCorr_semi import XmippProtStrGpuCrrSimple
-from .protocol_classification_gpuCorr_full import XmippProtStrGpuCrrCL2D
+#from .protocol_classify_kmeans2d import XmippProtKmeansClassif2D
 from .protocol_ctf_defocus_group import XmippProtCTFDefocusGroup
 from .protocol_compare_reprojections import XmippProtCompareReprojections
 from .protocol_compare_angles import XmippProtCompareAngles
@@ -51,7 +49,7 @@ from .protocol_create_gallery import XmippProtCreateGallery
 from .protocol_ctf_consensus import XmippProtCTFConsensus
 from .protocol_ctf_micrographs import XmippProtCTFMicrographs
 from .protocol_ctf_correct_wiener2d import XmippProtCTFCorrectWiener2D
-from .protocol_consensus_classes3D import XmippProtConsensusClasses3D
+from .protocol_consensus_classes import XmippProtConsensusClasses
 from .protocol_denoise_particles import XmippProtDenoiseParticles
 from .protocol_deep_micrograph_screen import  XmippProtDeepMicrographScreen
 from .protocol_eliminate_empty_images import (XmippProtEliminateEmptyParticles,
@@ -68,6 +66,7 @@ from .protocol_movie_gain import XmippProtMovieGain
 from .protocol_flexalign import XmippProtFlexAlign
 from .protocol_movie_opticalflow import XmippProtOFAlignment, ProtMovieAlignment
 from .protocol_movie_max_shift import XmippProtMovieMaxShift
+from .protocol_movie_dose_analysis import XmippProtMovieDoseAnalysis
 from .protocol_movie_split_frames import XmippProtSplitFrames
 from .protocol_multiple_fscs import XmippProtMultipleFSCs
 from .protocol_multireference_alignability import XmippProtMultiRefAlignability
@@ -75,7 +74,7 @@ from .protocol_normalize_strain import XmippProtNormalizeStrain
 from .protocol_particle_pick_automatic import XmippParticlePickingAutomatic
 from .protocol_particle_pick_consensus import XmippProtConsensusPicking
 from .protocol_pick_noise import XmippProtPickNoise
-from .protocol_particle_boxsize import XmippProtParticleBoxsize
+#from .protocol_particle_boxsize import XmippProtParticleBoxsize
 from .protocol_particle_pick import XmippProtParticlePicking
 from .protocol_particle_pick_pairs import XmippProtParticlePickingPairs
 from .protocol_phantom_create import XmippProtPhantom
@@ -96,7 +95,7 @@ from .protocol_resolution_monogenic_signal import XmippProtMonoRes
 from .protocol_resolution_deepres import XmippProtDeepRes
 from .protocol_postProcessing_deepPostProcessing import XmippProtDeepVolPostProc
 from .protocol_rotate_volume import XmippProtRotateVolume
-from .protocol_rotational_spectra import XmippProtRotSpectra
+#from .protocol_rotational_spectra import XmippProtRotSpectra
 from .protocol_rotational_symmetry import XmippProtRotationalSymmetry
 from .protocol_screen_particles import XmippProtScreenParticles
 from .protocol_screen_deepConsensus import XmippProtScreenDeepConsensus, XmippProtDeepConsSubSet
@@ -119,7 +118,6 @@ from .protocol_write_testC import XmippProtWriteTestC
 from .protocol_write_testP import XmippProtWriteTestP
 from .protocol_generate_reprojections import XmippProtGenerateReprojections
 from .protocol_deep_denoising import XmippProtDeepDenoising  # deepDenoising has to be after XmippProtGenerateReprojections and XmippProtCompareReprojections
-from .protocol_split_volume_hierarchical_cluster import XmippProtSplitVolumeHierarchical
 from .protocol_metaprotocol_create_subset import XmippMetaProtCreateSubset
 from .protocol_volume_deform_zernike3d import XmippProtVolumeDeformZernike3D
 from .protocol_structure_map_zernike3d import XmippProtStructureMapZernike3D
@@ -135,5 +133,7 @@ from .protocol_structure_map import XmippProtStructureMap
 from .protocol_apply_zernike3d import XmippApplyZernike3D
 from .protocol_volume_adjust_sub import XmippProtVolAdjust, XmippProtVolSubtraction
 from .protocol_volume_consensus import XmippProtVolConsensus
+from .protocol_volume_local_adjust import XmippProtLocalVolAdj
 from .protocol_classes_2d_mapping import XmippProtCL2DMap
 from .protocol_deep_hand import XmippProtDeepHand
+from .protocol_deep_center_assignment import XmippProtDeepCenter, XmippProtDeepGlobalAssignment

xmipp3/protocols/protocol_align_volume.py

@@ -32,6 +32,7 @@ from pwem.protocols import ProtAlignVolume
 from pwem.objects import Volume, Transform, SetOfVolumes
 
 from xmipp3.convert import getImageLocation
+from pyworkflow import BETA, UPDATED, NEW, PROD
 
 
 ALIGN_MASK_CIRCULAR = 0
@@ -51,6 +52,8 @@ class XmippProtAlignVolume(ProtAlignVolume):
      """
     _label = 'align volume'
     nVols = 0
+    _devStatus = PROD
+
     
     def __init__(self, **args):
         ProtAlignVolume.__init__(self, **args)
@@ -200,7 +203,9 @@ class XmippProtAlignVolume(ProtAlignVolume):
             fnOutVol = self._getExtraPath("vol%02d.mrc"%idx)
             outVol.setLocation(fnOutVol)
             outVol.setObjComment(vol.getObjComment())
-            #set transformation matrix             
+            outVol.setObjLabel(vol.getObjLabel())
+
+            #set transformation matrix
             fhInputTranMat = self._getExtraPath('transformation-matrix_vol%06d.txt'%idx)
             transMatFromFile = np.loadtxt(fhInputTranMat)
             transformationMat = np.reshape(transMatFromFile,(4,4))
@@ -329,7 +334,7 @@ class XmippProtAlignVolume(ProtAlignVolume):
         return maskArgs
     
     def _getAlignArgs(self):
-        alignArgs = ''
+        alignArgs = ' --dontWrap'
         
         if self.alignmentAlgorithm == ALIGN_ALGORITHM_FAST_FOURIER:
             alignArgs += " --frm"

xmipp3/protocols/protocol_align_volume_and_particles.py

@@ -256,7 +256,7 @@ class XmippProtAlignVolumeParticles(ProtAlignVolume):
             if self.maskType == ALIGN_MASK_CIRCULAR:
                 maskArgs+=" --mask circular -%d" % self.maskRadius
             else:
-                maskArgs+=" --mask binary_file %s" % self.volMask
+                maskArgs+=" --mask binary_file %s" % self.maskFile.get().getFileName()
         return maskArgs
 
           

xmipp3/protocols/protocol_analyze_local_ctf.py

@@ -34,6 +34,8 @@ from pwem.protocols import ProtAnalysis3D
 import pwem.emlib.metadata as md
 from xmipp3.convert import readSetOfMicrographs, writeSetOfMicrographs
 
+CITE ='Fernandez-Gimenez2023b'
+
 
 class XmippProtAnalyzeLocalCTF(ProtAnalysis3D):
     """Assigns to each micrograph a coefficient (R2) which evaluates the result of the