PtychoShelves
Contents:
PtychoShelves
template_ptycho - your virtual control room
How to add support for a beamline
base package documentation
ptycho package documentation
Academic License Agreement
PtychoShelves
Docs
»
Index
Index
Symbols
|
A
|
B
|
C
|
D
|
E
|
F
|
I
|
M
|
P
|
S
|
U
Symbols
+core (module)
+detector (module)
+engines (module)
+scans (module)
A
astra.add_to_3D() (built-in function)
astra.astra2matlab() (built-in function)
astra.ASTRA_find_optimal_split() (built-in function)
astra.Atx_partial() (built-in function)
astra.Ax_partial() (built-in function)
astra.iradon_gpu_wrapper() (built-in function)
astra.matlab2astra() (built-in function)
B
beamline.beamstop_mask() (built-in function)
beamline.choose_beamstop_mask() (built-in function)
beamline.create_mask() (built-in function)
beamline.create_mask_GUI_export() (built-in function)
beamline.energy2mark() (built-in function)
beamline.find_capillary() (built-in function)
beamline.find_specDatFile() (built-in function)
beamline.identify_eaccount() (built-in function)
beamline.ind2mask() (built-in function)
beamline.integrate_range() (built-in function)
beamline.intensity_calibration() (built-in function)
beamline.is_scan_finished() (built-in function)
beamline.is_scan_started() (built-in function)
beamline.mask2ind() (built-in function)
beamline.OMNY_get_scan_numbers() (built-in function)
beamline.pilatus_valid_pixel_roi() (built-in function)
beamline.prep_integ_masks() (built-in function)
beamline.prep_valid_mask() (built-in function)
beamline.radial_integ() (built-in function)
beamline.read_omny_angles() (built-in function)
beamline.read_omny_pos() (built-in function)
beamline.stxm_online() (built-in function)
beamline.tune_valid_mask() (built-in function)
C
core.append_engine() (built-in function)
(in module +core)
core.check_omny_queue() (in module +core)
core.check_prepared_data() (built-in function)
(in module +core)
core.engine_status() (built-in function)
(in module +core)
core.errorplot() (built-in function)
(in module +core)
core.export4remote() (built-in function)
core.extract4saving() (built-in function)
(in module +core)
core.find_shared_IDs() (built-in function)
core.FPM.align_data() (built-in function)
core.FPM.FP_prealign() (built-in function)
core.FPM.sort_pos() (built-in function)
core.FPM.sort_pos_radii() (built-in function)
core.generate_scan_name() (built-in function)
core.get_projections() (built-in function)
(in module +core)
core.hermite_like() (built-in function)
(in module +core)
core.initial_checks() (built-in function)
core.initialize_ptycho() (built-in function)
core.load_defaults() (built-in function)
core.plot_raw_data() (built-in function)
core.prep_h5data() (built-in function)
(in module +core)
core.prep_initial_conditions() (in module +core)
core.prep_initial_object() (built-in function)
core.prepare_data_matlab() (in module +core)
core.prepare_init_guess() (built-in function)
core.prepare_probes() (built-in function)
(in module +core)
core.probe_modes_ortho() (built-in function)
(in module +core)
core.ptycho_adjust_positions() (built-in function)
(in module +core)
core.ptycho_artificial_scans() (in module +core)
core.ptycho_exit() (built-in function)
core.ptycho_model_probe() (built-in function)
(in module +core)
core.ptycho_plot_ptycho() (built-in function)
(in module +core)
core.ptycho_prepare_paths() (built-in function)
core.ptycho_prepare_scans() (built-in function)
(in module +core)
core.ptycho_recons() (built-in function)
(in module +core)
core.python_prep_data() (in module +core)
core.remote_cleanup() (built-in function)
core.remote_status() (built-in function)
core.run_data_preparator() (built-in function)
core.run_engine() (built-in function)
(in module +core)
core.run_receiver() (built-in function)
core.save_fig_ext() (built-in function)
(in module +core)
core.save_results() (built-in function)
(in module +core)
core.set_projections() (built-in function)
core.update_omny_queue() (in module +core)
core.write_procID() (built-in function)
create_template() (built-in function)
cSAXS_python_env (module)
D
detector.eiger.eiger() (built-in function)
detector.eiger1p5M.convert() (built-in function)
detector.eiger1p5M.convert2hdf5() (built-in function)
detector.eiger1p5M.eiger1p5M() (built-in function)
detector.eiger4M_swing.eiger4M_swing() (built-in function)
detector.eiger9M.eiger9M() (built-in function)
detector.eiger9M.get_dir_path() (built-in function)
detector.initialize_detector() (built-in function)
(in module +detector)
detector.load_detector() (built-in function)
(in module +detector)
detector.moench.moench() (built-in function)
detector.oldeiger.oldeiger() (built-in function)
detector.pco_nano.pco_nano() (built-in function)
detector.pilatus.pilatus() (built-in function)
detector.prep_data.get_dir_path() (built-in function)
detector.prep_data.libDetXR.libDetXR() (built-in function)
detector.prep_data.matlab_ps.check_burst() (built-in function)
detector.prep_data.matlab_ps.get_center() (built-in function)
detector.prep_data.matlab_ps.get_mask() (built-in function)
detector.prep_data.matlab_ps.load_data() (built-in function)
detector.prep_data.matlab_ps.mask_geometry() (built-in function)
detector.prep_data.matlab_ps.matlab_ps() (built-in function)
detector.prep_data.matlab_ps.postprocess() (built-in function)
detector.prep_data.matlab_ps.prep_data_matlab() (built-in function)
detector.prep_data.matlab_ps.prepare_data() (built-in function)
detector.prep_data.matlab_ps.preprocess() (built-in function)
detector.prep_data.update_defaults() (built-in function)
detector.prep_data.update_funcs() (built-in function)
detector.prepare_data() (in module +detector)
detector.virtual.create_object() (built-in function)
detector.virtual.fourier_ptycho_data() (built-in function)
detector.virtual.get_center() (built-in function)
detector.virtual.load_data() (built-in function)
detector.virtual.preprocess() (built-in function)
detector.virtual.randpoisson() (built-in function)
detector.virtual.virtual() (built-in function)
E
engines.c_solver() (built-in function)
(in module +engines)
engines.c_solver.prep_initial_conditions() (built-in function)
engines.c_solver.prepare_external_call() (built-in function)
engines.c_solver_MS() (in module +engines)
engines.DM() (built-in function)
(in module +engines)
engines.DM_MS() (built-in function)
(in module +engines)
engines.GPU() (built-in function)
(in module +engines)
engines.GPU.add_momentum_object() (built-in function)
engines.GPU.add_momentum_probe() (built-in function)
engines.GPU.apply_probe_contraints() (built-in function)
engines.GPU.apply_smoothness_constraint() (built-in function)
engines.GPU.apply_SVD_filter() (built-in function)
engines.GPU.back_fourier_proj() (built-in function)
engines.GPU.calculate_conj_grad_dir() (built-in function)
engines.GPU.cat_struct() (built-in function)
engines.GPU.check_gpu_memory() (built-in function)
engines.GPU.clean_residua() (built-in function)
engines.GPU.distmat() (built-in function)
engines.GPU.extract_PCA() (built-in function)
engines.GPU.fft2_safe() (built-in function)
engines.GPU.find_geom_correction() (built-in function)
engines.GPU.find_reconstruction_ROI() (built-in function)
engines.GPU.flip_mirror_scan() (built-in function)
engines.GPU.fourier_ring_correlation() (built-in function)
engines.GPU.fsvd() (built-in function)
engines.GPU.fwd_fourier_proj() (built-in function)
engines.GPU.Garray() (built-in function)
engines.GPU.get_close_indices() (built-in function)
engines.GPU.get_forward_model() (built-in function)
engines.GPU.get_fourier_error() (built-in function)
engines.GPU.get_img_grad() (built-in function)
engines.GPU.get_mask() (built-in function)
engines.GPU.get_modulus() (built-in function)
engines.GPU.get_noise() (built-in function)
engines.GPU.get_nonoverlapping_indices() (built-in function)
engines.GPU.get_object_extent() (built-in function)
engines.GPU.get_optimal_LSQ_step() (built-in function)
engines.GPU.get_reciprocal_model() (built-in function)
engines.GPU.get_ROI() (built-in function)
engines.GPU.get_scanning_indices() (built-in function)
engines.GPU.get_variable_probe() (built-in function)
engines.GPU.get_views() (built-in function)
engines.GPU.Gfun() (built-in function)
engines.GPU.Ggather() (built-in function)
engines.GPU.Gpagefun() (built-in function)
engines.GPU.GPU_DM() (built-in function)
engines.GPU.GPU_LSQML() (built-in function)
engines.GPU.GPU_PIE() (built-in function)
engines.GPU.gpu_wrapper() (built-in function)
engines.GPU.gradient_descent_xi_solver() (built-in function)
engines.GPU.gradient_fourier_position_solver() (built-in function)
engines.GPU.gradient_NF_propagation_solver() (built-in function)
engines.GPU.gradient_position_solver() (built-in function)
engines.GPU.gradient_projection_solver() (built-in function)
engines.GPU.Gzeros() (built-in function)
engines.GPU.ifft2_safe() (built-in function)
engines.GPU.imagesc_hsv() (built-in function)
engines.GPU.initial_checks() (built-in function)
engines.GPU.initialize_solver() (built-in function)
engines.GPU.intersections() (built-in function)
engines.GPU.is_method() (built-in function)
engines.GPU.is_used() (built-in function)
engines.GPU.modulus_constraint() (built-in function)
engines.GPU.move_from_gpu() (built-in function)
engines.GPU.move_to_gpu() (built-in function)
engines.GPU.near_field_evolution() (built-in function)
engines.GPU.online_FSC_estimate() (built-in function)
engines.GPU.ortho_modes() (built-in function)
engines.GPU.ortho_modes_eig() (built-in function)
engines.GPU.plot_background_intensity() (built-in function)
engines.GPU.plot_frc_analysis() (built-in function)
engines.GPU.plot_geom_corrections() (built-in function)
engines.GPU.plot_intensity_corr() (built-in function)
engines.GPU.plot_object_modes() (built-in function)
engines.GPU.plot_probe_modes() (built-in function)
engines.GPU.plot_results() (built-in function)
engines.GPU.plot_variable_probe() (built-in function)
engines.GPU.precalculate_ROI() (built-in function)
engines.GPU.prepare_flyscan_positions() (built-in function)
engines.GPU.ptycho_solver() (built-in function)
engines.GPU.regulation_multilayers() (built-in function)
engines.GPU.rescale_inputs() (built-in function)
engines.GPU.set_views() (built-in function)
engines.GPU.set_views_rc() (built-in function)
engines.GPU.shift_probe() (built-in function)
engines.GPU.shift_probe_fft() (built-in function)
engines.GPU.show_spatial_distribution() (built-in function)
engines.GPU.update_variable_probe() (built-in function)
engines.ML() (built-in function)
(in module +engines)
engines.ML.brent() (built-in function)
engines.ML.cgmin1() (built-in function)
engines.ML.gradient_ptycho() (built-in function)
engines.ML.linesearch() (built-in function)
engines.ML_MS() (built-in function)
(in module +engines)
engines.ML_MS.fun_ramp_unwrap() (built-in function)
engines.ML_MS.gradient_ptycho_MS() (built-in function)
engines.ML_MS_rot() (built-in function)
engines.presolver() (built-in function)
(in module +engines)
F
fluo.geom_mat_blur() (built-in function)
fluo.geom_mat_simpler() (built-in function)
fluo.repeat() (built-in function)
fluo.replicate() (built-in function)
I
io.CBF.cbfread() (built-in function)
io.CBF.cbfwrite() (built-in function)
io.common_header_value() (built-in function)
io.datread() (built-in function)
io.edfread() (built-in function)
io.fliread() (built-in function)
io.HDF.add_content() (built-in function)
io.HDF.add_groups() (built-in function)
io.HDF.get_datatype() (built-in function)
io.HDF.hdf5_append_attr() (built-in function)
io.HDF.hdf5_attr_exists() (built-in function)
io.HDF.hdf5_cp_file() (built-in function)
io.HDF.hdf5_dset_exists() (built-in function)
io.HDF.hdf5_load() (built-in function)
io.HDF.hdf5_mv_data() (built-in function)
io.HDF.hdf5_rm_attr() (built-in function)
io.HDF.hdf5_rm_data() (built-in function)
io.HDF.hdf5read_main() (built-in function)
io.HDF.rm_delimiter() (built-in function)
io.HDF.save2hdf5() (built-in function)
io.HDF.write_attribute() (built-in function)
io.HDF.write_dataset() (built-in function)
io.image_info() (built-in function)
io.image_orient() (built-in function)
io.image_orient_help() (built-in function)
io.image_read() (built-in function)
io.image_read_help() (built-in function)
io.image_read_sub_help() (built-in function)
io.json2mat() (built-in function)
io.load_prepared_data() (built-in function)
io.load_ptycho_recons() (built-in function)
io.marread() (built-in function)
io.mat2json() (built-in function)
io.mcs_mesh() (built-in function)
io.multiple_mcs_headers() (built-in function)
io.read_scan_positions_spec() (built-in function)
io.save_append() (built-in function)
io.savefast_safe() (built-in function)
io.sendSMS() (built-in function)
io.spec_help() (built-in function)
io.spec_read() (built-in function)
io.speread() (built-in function)
M
math.argmax() (built-in function)
math.argmin() (built-in function)
math.center() (built-in function)
math.double2int() (built-in function)
math.fft2_partial() (built-in function)
math.fft_partial() (built-in function)
math.fftn_partial() (built-in function)
math.fftshift_2D() (built-in function)
math.fsvd() (built-in function)
math.get_img_grad() (built-in function)
math.get_img_int_1D() (built-in function)
math.get_img_int_2D() (built-in function)
math.get_phase_gradient_1D() (built-in function)
math.get_phase_gradient_2D() (built-in function)
math.ifft2_partial() (built-in function)
math.ifft_partial() (built-in function)
math.ifftn_partial() (built-in function)
math.ifftshift_2D() (built-in function)
math.isint() (built-in function)
math.legendrepoly1D_2() (built-in function)
math.max2() (built-in function)
math.mean2() (built-in function)
math.min2() (built-in function)
math.nnorm() (built-in function)
math.norm2() (built-in function)
math.peakfit2d() (built-in function)
math.projectleg1D_2() (built-in function)
math.sp_quantile() (built-in function)
math.sum2() (built-in function)
math.unwrap2D_fft() (built-in function)
math.unwrap2D_fft2() (built-in function)
P
plotting.banana_plot() (built-in function)
plotting.c2image() (built-in function)
plotting.display_integ_masks() (built-in function)
plotting.display_valid_mask() (built-in function)
plotting.franzmap() (built-in function)
plotting.ginput_ax_mod2() (built-in function)
plotting.hline() (built-in function)
plotting.image_show() (built-in function)
plotting.image_spec() (built-in function)
plotting.imagesc3D() (built-in function)
plotting.imagesc_tomo() (built-in function)
plotting.integrate_frames() (built-in function)
plotting.integrated_intensity() (built-in function)
plotting.plot_radial_integ() (built-in function)
plotting.ptycho_show_recons() (built-in function)
plotting.scan_movie() (built-in function)
plotting.spec_plot() (built-in function)
plotting.suptitle() (built-in function)
plotting.tight_subplot() (built-in function)
plotting.vline() (built-in function)
S
scans.get_filenames_cSAXS() (built-in function)
scans.get_queue() (built-in function)
(in module +scans)
scans.meta.artificial() (built-in function)
scans.meta.nexus() (built-in function)
scans.meta.spec() (built-in function)
scans.positions.load_from_file() (built-in function)
scans.positions.matlab_pos() (built-in function)
scans.positions.nexus_soleil() (built-in function)
scans.positions.orchestra() (built-in function)
scans.positions.spec() (built-in function)
scans.queue.check_queue.lockfile() (built-in function)
scans.queue.check_queue.omny() (built-in function)
scans.queue.check_queue.ptycho_parse_omny_dat() (built-in function)
scans.queue.check_queue.remote_queue() (built-in function)
scans.queue.update_queue.omny() (built-in function)
scans.queue.update_queue.remote_queue() (built-in function)
scans.read_metadata() (built-in function)
(in module +scans)
scans.read_positions() (built-in function)
(in module +scans)
setup_recons() (built-in function)
setup_remote_recons() (built-in function)
setup_template() (built-in function)
U
utils (module)
utils.abspath() (built-in function)
utils.add_to_3D_projection() (built-in function)
utils.adjust_projection() (built-in function)
utils.auto_mask_find() (built-in function)
utils.binning_2D() (built-in function)
utils.binning_3D() (built-in function)
utils.char_to_cellstr() (built-in function)
utils.check_available_memory() (built-in function)
utils.check_cpu_load() (built-in function)
utils.check_matlab_version() (built-in function)
utils.check_perm() (built-in function)
utils.compile_x12sa_dirname() (built-in function)
utils.compile_x12sa_filename() (built-in function)
utils.crop_pad() (built-in function)
utils.dftregistration() (built-in function)
utils.dose_calc() (built-in function)
utils.filt2d() (built-in function)
utils.filt2d_pad() (built-in function)
utils.find_files() (built-in function)
utils.find_latest_file() (built-in function)
utils.find_package_refs() (built-in function)
utils.findresidues() (built-in function)
utils.focus_series_fit() (built-in function)
utils.fopen_until_exists() (built-in function)
utils.fourier_shell_corr_3D_2() (built-in function)
utils.fract_hanning() (built-in function)
utils.fract_hanning_pad() (built-in function)
utils.get_att_length() (built-in function)
utils.get_beam_center() (built-in function)
utils.get_fil_trans() (built-in function)
utils.get_from_3D_projection() (built-in function)
utils.get_gas_trans() (built-in function)
utils.get_grid() (built-in function)
utils.get_hdr_val() (built-in function)
utils.get_option() (built-in function)
utils.get_ref_index() (built-in function)
utils.goldstein_unwrap2D() (built-in function)
utils.goldsteinunwrap2() (built-in function)
utils.identify_system() (built-in function)
utils.imdeform_affine_fft() (built-in function)
utils.imgaussfilt2_fft() (built-in function)
utils.imgaussfilt3_conv() (built-in function)
utils.imgaussfilt3_fft() (built-in function)
utils.imrescale_fft() (built-in function)
utils.imrescale_frft() (built-in function)
utils.imrotate_ax() (built-in function)
utils.imrotate_ax_fft() (built-in function)
utils.imshear_fft() (built-in function)
utils.imshift_ax() (built-in function)
utils.imshift_fast() (built-in function)
utils.imshift_fft() (built-in function)
utils.imshift_fft_ax() (built-in function)
utils.interpolate_linear() (built-in function)
utils.interpolateFT() (built-in function)
utils.interpolateFT_ax() (built-in function)
utils.onCleanup() (built-in function)
utils.param_protect_field() (built-in function)
utils.peakfinder() (built-in function)
utils.pixel_to_q() (built-in function)
utils.power_spectral_density() (built-in function)
utils.progressbar() (built-in function)
utils.prop2focus() (built-in function)
utils.prop_free_ff() (built-in function)
utils.prop_free_nf() (built-in function)
utils.pshift() (built-in function)
utils.registersubimages_2() (built-in function)
utils.relative_path() (built-in function)
utils.remove_linear_phase_smart() (built-in function)
utils.remove_linearphase() (built-in function)
utils.remove_linearphase_v2() (built-in function)
utils.remove_sinogram_ramp() (built-in function)
utils.rmphaseramp() (built-in function)
utils.savefast_safe() (built-in function)
utils.sbb() (built-in function)
utils.shiftpp2() (built-in function)
utils.shiftwrapbilinear() (built-in function)
utils.smooth_edges() (built-in function)
utils.stabilize_phase() (built-in function)
utils.struc2cell() (built-in function)
utils.update_param() (built-in function)
utils.verbose() (built-in function)