scipion-em-xmipp 23.7.0.0__py3-none-any.whl → 23.11.0.0__py3-none-any.whl

{scipion_em_xmipp-23.7.0.0.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: 23.7.0.0
+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: scikit-learn (==0.22)
+Requires-Dist: scipion-pyworkflow >=3.0.31
+Requires-Dist: scikit-learn ==0.22
 Requires-Dist: scipion-em
-Requires-Dist: scipy (<=1.10.0)
+Requires-Dist: scipy <=1.10.0
 Requires-Dist: joblib
 Requires-Dist: peppercorn
 Requires-Dist: plotter

{scipion_em_xmipp-23.7.0.0.dist-info → scipion_em_xmipp-23.11.0.0.dist-info}/RECORD

@@ -1,20 +1,20 @@
-xmipp3/__init__.py,sha256=uRFVuqU3j5VIpsSkyNx13GTTFLfngD8-3echpzsXjLI,13059
+xmipp3/__init__.py,sha256=QuKgvzbrckW-olA05xkWEbz5L9rMOvBFbTj3Nmt2hcg,13311
 xmipp3/base.py,sha256=pFu7FZjm4WeqWbLZJwbmGH3-2YixAIpKyWMFvVrsBYc,21220
-xmipp3/bibtex.py,sha256=vl6W2EnjcRT4Iobc0YlMOpLE3SkjQLv_VcQnaHrLz50,26889
+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=-OO3A25O4g0_0igPnhaITlZZ0HZfvsr1fiFSqjqgFeM,12540
+xmipp3/protocols.conf,sha256=oyp24nsLnr5TqjLVgPIfJjEwD9QlQ1MCzwuUAj_mlJ0,12386
 xmipp3/utils.py,sha256=JKuEdR40rn6pdm0puwsgzItbNnrFL4sa7pBymVtRzLM,9125
 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=R32KOUqU9uVlXy7qc9LCZGHoRyn0Nz85LXwBEBkDcZ0,8896
-xmipp3/protocols/protocol_align_volume.py,sha256=prrzzFJUiyuRJmIIHtIRgcG5A3-c9PwJnKxKjN5ZHkU,19073
+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=IfiHD8TGOQT4mogtqJqpVXzcrcfv0Svw-oIJkCEVXh4,7414
+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
@@ -26,44 +26,38 @@ xmipp3/protocols/protocol_center_particles.py,sha256=2ug42YlvD7PidOLC1EL6U4b-WFm
 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_compare_angles.py,sha256=NIoQjym4aH3BsMJ7RaMmyswEl9gHkxMnnkQQJdAQaCw,8034
 xmipp3/protocols/protocol_compare_reprojections.py,sha256=nRDA9tvF9wATuNZW7PoQ6H5N9CKDiKnwPeYyxgsG4ug,15333
-xmipp3/protocols/protocol_consensus_classes.py,sha256=v6Q1pC7NIOeXB-Oeg69j1yebqxIBi58GGbBYqq7Ew2w,25092
-xmipp3/protocols/protocol_consensus_local_ctf.py,sha256=X2xOP9i2E8SMU8JR6huARsi6qss6QJg0Kslbw0iF_IE,9925
-xmipp3/protocols/protocol_convert_pdb.py,sha256=PCukDhaE2ExhJOqcV7TxBJ-nJh3K-QuExnl7PitcLAU,14775
+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=W8037NXcdlodnQmBY3vvWKJswXGjF1c5JYLZ5JiLOeE,42614
+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.py,sha256=dF_4q0nsVhDKeQS822aPT2Le1PVLPySbpl6breExThY,8167
-xmipp3/protocols/protocol_deep_center_predict.py,sha256=efCN34VnKbjsD2p1-uVhCnyspbl9k7WckKTCtZ3JwCw,6916
+xmipp3/protocols/protocol_deep_center_assignment.py,sha256=87rh6bdYfbOViEn0atEzahwD0ON5Yp4PPBSg-dyCbzk,12691
 xmipp3/protocols/protocol_deep_denoising.py,sha256=z7lkqP8AylC1NMbHkGORUKLAiS9DAffInaZUpbYAAVo,21324
-xmipp3/protocols/protocol_deep_global_assignment.py,sha256=h6n7kZ7mfVtUHHZmX0iG8_feIb8XUTqBARtFnPn4tcg,8218
-xmipp3/protocols/protocol_deep_global_assignment_predict.py,sha256=rXWrZoB7VjOVEtbalS8LfBUtSaeE97lFYct4fwAhp30,6690
 xmipp3/protocols/protocol_deep_hand.py,sha256=KeKV6DHqpua1GoL3dWojYhwAHEiUxXy5Mdkr0at77ag,7185
-xmipp3/protocols/protocol_deep_micrograph_screen.py,sha256=yY5-Yvnro_LEvFwoWd2Pnsr4dQVEAr2bFu4h3hntnQM,22168
+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=sVObw67jj9Nhm3HBbB5T8FQ6aZawNEzS2-td_6Y95l4,18472
+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_local_ctf.py,sha256=83Yl_S_AD8_wFzGhvdA36TsIMzraWm0KpuOUFqkEdWA,8078
+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_dose_analysis.py,sha256=53tKhS2CkG7CRGuGTLxc9VCgm0sNifqzejqhzqjuzt8,17826
-xmipp3/protocols/protocol_movie_gain.py,sha256=Q97hS6zNf9Jg-XV--HZlIHehcKLd5j9o8_WV1IA4tqs,25732
+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
@@ -71,14 +65,14 @@ xmipp3/protocols/protocol_multiple_fscs.py,sha256=Q-F-gZIIk8V8jtMB1DW1R2RbDvXloS
 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_pick.py,sha256=Kk75_SEv12796oOaRL1u80hsNzV1nzFfiOcryAxaT3Y,9784
-xmipp3/protocols/protocol_particle_pick_automatic.py,sha256=D8B-UBifaBBuv4b4NpRHRoo3ziI5IHnvjSWInzGd2t4,10864
-xmipp3/protocols/protocol_particle_pick_consensus.py,sha256=5X60sFnE9ipZs8P4q0TBuZYYmVHL74wBSDwI4PoH6BU,16901
+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
@@ -87,13 +81,13 @@ 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_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=bRJFK10etEP3ztCK8XWssaeECJvbVWYrm2ct3S4sRK4,17148
+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_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
@@ -103,16 +97,17 @@ xmipp3/protocols/protocol_solid_angles.py,sha256=taET1k3d0v-mUi2fq4cUn8AvWygg7Iq
 xmipp3/protocols/protocol_split_volume.py,sha256=4yfrx8BKzMszgZijqJ3iEAHD66DWlVNm4rwWwwsvhTE,5928
 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=XdAC7VOOZGyrK4ING6IW2Puo_BN-FnW1mOzMMwtuXkc,12820
-xmipp3/protocols/protocol_tilt_analysis.py,sha256=ZTLnDn8ZVcFhRSpPYx--9KdmtIMZsJzNXmZEgRUVrXo,27993
-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
@@ -121,12 +116,12 @@ xmipp3/protocols/protocol_preprocess/geometrical_mask.py,sha256=8ZFzffgXlSsth83X
 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=EkEzJJZTBwmMRa5j5jYy22gbIvOESyjGSkxPHgk7Atc,18818
-xmipp3/protocols/protocol_preprocess/protocol_crop_resize.py,sha256=8-BuZx6MZpnI6YsnWRVQjjgcN2EmfMH-fE93Jenm70c,25599
-xmipp3/protocols/protocol_preprocess/protocol_filter.py,sha256=obIGVFbp71l38ftAFFRBMGT0swTtttyOBjvnm0dSwME,22928
+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_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
@@ -140,11 +135,8 @@ 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.py,sha256=fK06BVkRT2Sccokp9GR4fv3M9ZBzYITHHPF5n2KGIi8,4403
-xmipp3/tests/test_protocol_deep_center_predict.py,sha256=Ed1hWMwjh4UFfZVnA856Nq60he1TK_b3NEGczM_N-64,3800
+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_deep_global_assignment.py,sha256=wdgQkR64NomT20V7wtmZQDsGG_N33MK0VIwQBsZCS4A,4414
-xmipp3/tests/test_protocol_deep_global_assignment_predict.py,sha256=NPNfC5sB-dRDC8R5q8LsrUFFdePY77p4tgYAbuuV_CE,3819
 xmipp3/tests/test_protocol_extract_asymmetric_unit.py,sha256=Ya8zy3wuKi10r-_LVwpavYgzVrGy-5M3Gy05MHNmr7M,23298
 xmipp3/tests/test_protocol_monodir.py,sha256=nt-5KEzbVAtsNeQ9OOifYSp1kN2N7tZwxtwS1ipbljY,3741
 xmipp3/tests/test_protocol_multiple_fsc.py,sha256=E7rhBJI9qJXAnbuxARK9auwnMxmYtIxS8PVi3TT2yj4,4012
@@ -160,26 +152,23 @@ xmipp3/tests/test_protocols_continuousflex.py,sha256=y_WeCm-XiZ5rJS1lx4i0TsGoWNf
 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=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=rl9QrVth3-VnXfxAYq-nYdYdgLcP_hy8Kmv5iLz_jcw,75260
-xmipp3/tests/test_protocols_xmipp_3d.py,sha256=DD2GK_RZEmj7-13thRwD9IisIGx0ctirHBD2uQRxwO0,166280
-xmipp3/tests/test_protocols_xmipp_mics.py,sha256=gorFkFxsbgPmf8_P3To5hWB4B9WFnO7l9Qp1GiHEQCs,59829
+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=SFn8sZyFl3ROatSWCl4CmhKA1nAkygJDNQFgFe0r2sY,38274
 xmipp3/tests/test_protocols_zernike3d.py,sha256=bTXCK4wBKSJZK1KCZXec3j8y1mVLoBxE5bF3AGbOsNs,18132
 xmipp3/viewers/__init__.py,sha256=gHkUPN2FOp-vvoLRcZzoHjatMNdmBTWp6607pnjaQsI,3618
 xmipp3/viewers/plotter.py,sha256=YHDqAs7_rbv8cXMmwmg42YeeBnesdX44awrppX3VJw0,3875
-xmipp3/viewers/viewer.py,sha256=K_f553ewBHse8aBfjN3AZwAnZNCfl3dhil-7_P-P_CU,19690
+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
@@ -203,7 +192,7 @@ xmipp3/viewers/viewer_reconstruct_highres.py,sha256=bDcxUyGU4wlRFdBnfbhMiCLRB8b_
 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_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
@@ -218,9 +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-23.7.0.0.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-scipion_em_xmipp-23.7.0.0.dist-info/METADATA,sha256=W8Li8Db_LIjeBwdspnfM1jM4qKQOQCBDjoI1lphxdWQ,1627
-scipion_em_xmipp-23.7.0.0.dist-info/WHEEL,sha256=pkctZYzUS4AYVn6dJ-7367OJZivF2e8RA9b_ZBjif18,92
-scipion_em_xmipp-23.7.0.0.dist-info/entry_points.txt,sha256=uAfbaIdLcZ7JWL0tWzQVwsVEyyOZb1WcBX4YZMqRrIk,37
-scipion_em_xmipp-23.7.0.0.dist-info/top_level.txt,sha256=qnLFoZzwKticb33xgeSAJv3P7nD2nHMTFKYzxAorOOQ,7
-scipion_em_xmipp-23.7.0.0.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-23.7.0.0.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"
+type_of_version = 'release' #'devel'
+_logo = "xmipp_logo" + ("" if type_of_version == 'release' else '_devel') + '.png'
+
 _references = ['delaRosaTrevin2013', 'Sorzano2013', 'Strelak2021']
-_currentBinVersion = '3.23.07.0'
+_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
@@ -209,12 +212,12 @@ def installDeepLearningToolkit(plugin, env):
                                                env=plugin.getEnviron(),
                                                stdout=subprocess.PIPE
                                                ).stdout.read().decode('utf-8').split(".")[0]
-            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)."
-                                "To enable CUDA (drivers>390 needed), "
+                                f"To enable CUDA (drivers>{NVIDIA_DRIVERS_MINIMUM_VERSION} needed), "
                                 "set CUDA=True in 'scipion.conf' file")
                 nvidiaDriverVer = None
         except (ValueError, TypeError):
@@ -239,7 +242,7 @@ def installDeepLearningToolkit(plugin, env):
     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",

xmipp3/bibtex.py

@@ -620,5 +620,43 @@ 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

@@ -40,9 +40,6 @@ 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_ctf_defocus_group import XmippProtCTFDefocusGroup
 from .protocol_compare_reprojections import XmippProtCompareReprojections
 from .protocol_compare_angles import XmippProtCompareAngles
@@ -136,9 +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 import XmippProtDeepCenter
-from .protocol_deep_center_predict import XmippProtDeepCenterPredict
-from .protocol_deep_global_assignment import XmippProtDeepGlobalAssignment
-from .protocol_deep_global_assignment_predict import XmippProtDeepGlobalAssignmentPredict
+from .protocol_deep_center_assignment import XmippProtDeepCenter, XmippProtDeepGlobalAssignment

xmipp3/protocols/protocol_align_volume.py

@@ -52,7 +52,7 @@ class XmippProtAlignVolume(ProtAlignVolume):
      """
     _label = 'align volume'
     nVols = 0
-    _devStatus = UPDATED
+    _devStatus = PROD
 
     
     def __init__(self, **args):

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

xmipp3/protocols/protocol_consensus_classes.py

@@ -164,18 +164,6 @@ class XmippProtConsensusClasses(ProtClassify3D):
         self._writeElbows(elbows)
 
     # --------------------------- INFO functions -------------------------------
-    """
-    def _validate(self):
-        errors = []
-
-        # Ensure that all classifications are made of the same images
-        items = self._getInputImages(0)
-        for i in range(1, len(self.inputClassifications)):
-            if self._getInputImages(i) != items:
-                errors.append(f'Classification {i} has been done with different images')
-
-        return errors
-    """
     
     # --------------------------- UTILS functions ------------------------------
     def _getInputClassificationCount(self) -> int:
@@ -479,7 +467,6 @@ class XmippProtConsensusClasses(ProtClassify3D):
             mu2 = np.mean(d2)
             sigma1 = np.std(d1, ddof=1)
             sigma2 = np.std(d2, ddof=1)
-            #sigma = (len(d1)*sigma1 + len(d2)*sigma2) / (len(d1) + len(d2)) # Weighted average
         
             # Compute the log likelihood
             logLikelihoods1 = scipy.stats.norm.logpdf(d1, mu1, sigma1)

xmipp3/protocols/protocol_consensus_local_ctf.py

@@ -40,11 +40,12 @@ from xmipp3.convert import setXmippAttribute
 from pyworkflow import BETA, UPDATED, NEW, PROD
 
 OUTPUTNAME = "outputParticles"
+CITE ='Fernandez-Gimenez2023b'
 
 class XmippProtConsensusLocalCTF(ProtAnalysis3D):
     """This protocol compares the estimations of local defocus computed by different protocols for a set of particles"""
     _label = 'consensus local defocus'
-    _devStatus = UPDATED
+    _devStatus = PROD
 
     _lastUpdateVersion = VERSION_2_0
     _possibleOutputs = {OUTPUTNAME:SetOfParticles}

xmipp3/protocols/protocol_convert_pdb.py

@@ -28,6 +28,9 @@
 # *
 # **************************************************************************
 
+# General imports
+import os
+
 # Scipion em imports
 from pwem.convert.headers import setMRCSamplingRate
 from pwem.emlib.image import ImageHandler
@@ -37,7 +40,7 @@ from pwem.protocols import ProtInitialVolume
 import pyworkflow.protocol.params as params
 import pyworkflow.protocol.constants as const
 from pyworkflow.utils import replaceBaseExt, removeExt, getExt, createLink, replaceExt, removeBaseExt
-from pyworkflow import BETA, UPDATED, NEW, PROD
+from pyworkflow import UPDATED
 
 class XmippProtConvertPdb(ProtInitialVolume):
     """ Convert atomic structure(s) into volume(s) """
@@ -70,7 +73,7 @@ class XmippProtConvertPdb(ProtInitialVolume):
         coordsCondition = 'setSize and not vol'
 
         # Defining parallel arguments
-        form.addParallelSection(threads=4)
+        form.addParallelSection(threads=4, mpi=1)
 
         # Generating form
         form.addSection(label='Input')
@@ -102,12 +105,16 @@ class XmippProtConvertPdb(ProtInitialVolume):
         form.addParam('centerPdb', params.BooleanParam, default=True,
                       expertLevel=const.LEVEL_ADVANCED, 
                       label="Center PDB",
-                      help='Center PDB with the center of mass')
+                      help='Center PDB with the center of mass.')
         form.addParam('outPdb', params.BooleanParam, default=False, 
                       expertLevel=const.LEVEL_ADVANCED, 
                       label="Store centered PDB",
                       help='Set to \'Yes\' if you want to save centered PDB. '
-                           'It will be stored in the output directory of this protocol')
+                           'It will be stored in the output directory of this protocol.')
+        form.addParam('convertCif', params.BooleanParam, default=True,
+                      expertLevel=const.LEVEL_ADVANCED, 
+                      label="Convert CIF to PDB",
+                      help='If set to true and input atom struct file is a CIF, it will get converted to PDB.')
         form.addParam('clean', params.BooleanParam, default=True,
                       expertLevel=const.LEVEL_ADVANCED, 
                       label="Clean tmp files",
@@ -138,8 +145,8 @@ class XmippProtConvertPdb(ProtInitialVolume):
     # --------------------------- STEPS functions --------------------------------------------
     def processConversion(self, pdb, samplingR, isSet):
         """ This step runs the pdb conversion. """
-        # Converting all input atomic structures to .pdb
-        pdb = self._convertToPdb(pdb)
+        # Conditionally converting all input atomic structures to .pdb
+        pdb = self._convertAtomStruct(pdb)
         
         # Generating output file for each input
         outFile = removeExt(pdb)
@@ -260,13 +267,14 @@ class XmippProtConvertPdb(ProtInitialVolume):
             # If it is a SetOfAtom Structs, get all of the elements iterating the set
             return [i.getFileName() for i in pbdObj]
 
-    def _convertToPdb(self, pdbRaw):
-        """ This function receives an atomic struct file, and converts it to .pdb if it is in .cif format. """
-        # Get output path for pdb file
-        convertedPdb = self._getExtraPath(replaceBaseExt(pdbRaw, 'pdb')).replace(" ", "_")
+    def _convertAtomStruct(self, pdbRaw):
+        """ This function receives an atomic struct file, and conditionally converts it to .pdb if it is in .cif format. """
+        # Get output path for atomic struct file
+        baseExt = replaceBaseExt(pdbRaw, 'pdb') if self.convertCif.get() else os.path.basename(pdbRaw)
+        convertedPdb = self._getExtraPath(baseExt).replace(" ", "_")
 
-        # If file extension is .cif, convert to .pdb, or else we link it as is
-        if getExt(pdbRaw) == ".cif":
+        # If file extension is .cif and conversion is required, convert to .pdb, or else we link it as is
+        if getExt(pdbRaw) == ".cif" and self.convertCif.get():
             cifToPdb(pdbRaw, convertedPdb)
         else:
             createLink(pdbRaw, convertedPdb)

xmipp3/protocols/protocol_create_gallery.py

@@ -51,7 +51,7 @@ class XmippProtCreateGallery(ProtAnalysis3D):
         form.addParam('symmetryGroup', StringParam, default="c1",
                       label='Symmetry group', 
                       help='See'
-                           'http://xmipp.cnb.uam.es/twiki/bin/view/Xmipp/Symmetry '
+                           'https://github.com/I2PC/xmipp-portal/wiki/Symmetry '
                            'for a description of the symmetry groups format. '
                            'If no symmetry is present, give c1')
 

xmipp3/protocols/protocol_ctf_consensus.py

@@ -59,7 +59,7 @@ class XmippProtCTFConsensus(ProtCTFMicrographs):
     the agreement with a secondary CTF for the same set of micrographs.
     """
     _label = 'ctf consensus'
-    _devStatus = UPDATED
+    _devStatus = PROD
     _lastUpdateVersion = VERSION_3_0
 
     def __init__(self, **args):
@@ -200,12 +200,11 @@ class XmippProtCTFConsensus(ProtCTFMicrographs):
             self.ctfFn2 = self.inputCTF2.get().getFileName()
             self.allCtf2 = {}
 
-        ctfSteps = self._checkNewInput()
         self._insertFunctionStep('createOutputStep',
-                                 prerequisites=ctfSteps, wait=True)
+                                 prerequisites=[], wait=True)
 
     def createOutputStep(self):
-        pass
+        self._closeOutputSet()
 
     def initializeParams(self):
         self.finished = False