Merge pull request #83 from NSLS-II/updates-20240429-with-style-fixes

Updates 20240429 with style fixes

.pre-commit-config.yaml

@@ -1,22 +1,23 @@
+exclude: '(v2)/.*'
 default_language_version:
     python: python3
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.6.0
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
   - repo: https://github.com/ambv/black
-    rev: 23.1.0
+    rev: 24.4.2
     hooks:
       - id: black
   - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
         args: ["--profile", "black"]
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.6.1
+    rev: 0.7.1
     hooks:
       - id: nbstripout

chx_packages_local.py

@@ -0,0 +1,315 @@
+### This enables local import of pyCHX for testing
+
+import pickle as cpk
+
+import historydict
+
+# from pyCHX.chx_handlers import use_dask, use_pims
+from chx_handlers import use_dask, use_pims
+
+# from pyCHX.chx_libs import (
+from chx_libs import (
+    EigerHandler,
+    Javascript,
+    LogNorm,
+    Model,
+    cmap_albula,
+    cmap_vge,
+    datetime,
+    db,
+    getpass,
+    h5py,
+    multi_tau_lags,
+    np,
+    os,
+    pims,
+    plt,
+    random,
+    roi,
+    time,
+    tqdm,
+    utils,
+    warnings,
+)
+from eiger_io.fs_handler import EigerImages
+from skimage.draw import line, line_aa, polygon
+
+# changes to current version of chx_packages.py
+# added load_dask_data in generic_functions
+
+
+use_pims(db)  # use pims for importing eiger data, register_handler 'AD_EIGER2' and 'AD_EIGER'
+
+# from pyCHX.chx_compress import (
+from chx_compress import (
+    MultifileBNLCustom,
+    combine_binary_files,
+    create_compress_header,
+    para_compress_eigerdata,
+    para_segment_compress_eigerdata,
+    segment_compress_eigerdata,
+)
+
+# from pyCHX.chx_compress_analysis import (
+from chx_compress_analysis import (
+    Multifile,
+    cal_each_ring_mean_intensityc,
+    cal_waterfallc,
+    compress_eigerdata,
+    get_avg_imgc,
+    get_each_frame_intensityc,
+    get_each_ring_mean_intensityc,
+    get_time_edge_avg_img,
+    mean_intensityc,
+    plot_each_ring_mean_intensityc,
+    plot_waterfallc,
+    read_compressed_eigerdata,
+)
+
+# from pyCHX.chx_correlationc import Get_Pixel_Arrayc, auto_two_Arrayc, cal_g2c, get_pixelist_interp_iq
+from chx_correlationc import Get_Pixel_Arrayc, auto_two_Arrayc, cal_g2c, get_pixelist_interp_iq
+
+# from pyCHX.chx_correlationp import _one_time_process_errorp, auto_two_Arrayp, cal_g2p, cal_GPF, get_g2_from_ROI_GPF
+from chx_correlationp import _one_time_process_errorp, auto_two_Arrayp, cal_g2p, cal_GPF, get_g2_from_ROI_GPF
+
+# from pyCHX.chx_crosscor import CrossCorrelator2, run_para_ccorr_sym
+from chx_crosscor import CrossCorrelator2, run_para_ccorr_sym
+
+# from pyCHX.chx_generic_functions import (
+from chx_generic_functions import (
+    R_2,
+    RemoveHot,
+    apply_mask,
+    average_array_withNan,
+    check_bad_uids,
+    check_lost_metadata,
+    check_ROI_intensity,
+    check_shutter_open,
+    combine_images,
+    copy_data,
+    create_cross_mask,
+    create_fullImg_with_box,
+    create_hot_pixel_mask,
+    create_multi_rotated_rectangle_mask,
+    create_polygon_mask,
+    create_rectangle_mask,
+    create_ring_mask,
+    create_seg_ring,
+    create_time_slice,
+    create_user_folder,
+    delete_data,
+    extract_data_from_file,
+    filter_roi_mask,
+    find_bad_pixels,
+    find_bad_pixels_FD,
+    find_good_xpcs_uids,
+    find_index,
+    find_uids,
+    fit_one_peak_curve,
+    get_averaged_data_from_multi_res,
+    get_avg_img,
+    get_bad_frame_list,
+    get_base_all_filenames,
+    get_cross_point,
+    get_current_pipeline_filename,
+    get_current_pipeline_fullpath,
+    get_curve_turning_points,
+    get_detector,
+    get_detectors,
+    get_each_frame_intensity,
+    get_echos,
+    get_eigerImage_per_file,
+    get_fit_by_two_linear,
+    get_fra_num_by_dose,
+    get_g2_fit_general,
+    get_image_edge,
+    get_image_with_roi,
+    get_img_from_iq,
+    get_last_uids,
+    get_mass_center_one_roi,
+    get_max_countc,
+    get_meta_data,
+    get_multi_tau_lag_steps,
+    get_non_uniform_edges,
+    get_print_uids,
+    get_q_rate_fit_general,
+    get_qval_dict,
+    get_qval_qwid_dict,
+    get_roi_mask_qval_qwid_by_shift,
+    get_roi_nr,
+    get_series_g2_taus,
+    get_SG_norm,
+    get_sid_filenames,
+    get_today_date,
+    get_touched_qwidth,
+    get_waxs_beam_center,
+    lin2log_g2,
+    linear_fit,
+    load_dask_data,
+    load_data,
+    load_mask,
+    load_pilatus,
+    ls_dir,
+    mask_badpixels,
+    mask_exclude_badpixel,
+    move_beamstop,
+    pad_length,
+    pload_obj,
+    plot1D,
+    plot_fit_two_linear_fit,
+    plot_g2_general,
+    plot_q_g2fitpara_general,
+    plot_q_rate_fit_general,
+    plot_q_rate_general,
+    plot_xy_with_fit,
+    plot_xy_x2,
+    print_dict,
+    psave_obj,
+    read_dict_csv,
+    refine_roi_mask,
+    reverse_updown,
+    ring_edges,
+    run_time,
+    save_array_to_tiff,
+    save_arrays,
+    save_current_pipeline,
+    save_dict_csv,
+    save_g2_fit_para_tocsv,
+    save_g2_general,
+    save_lists,
+    save_oavs_tifs,
+    sgolay2d,
+    shift_mask,
+    show_img,
+    show_ROI_on_image,
+    shrink_image,
+    trans_data_to_pd,
+    update_qval_dict,
+    update_roi_mask,
+    validate_uid,
+)
+
+# from pyCHX.chx_olog import Attachment, LogEntry, update_olog_id, update_olog_uid, update_olog_uid_with_file
+from chx_olog import Attachment, LogEntry, update_olog_id, update_olog_uid, update_olog_uid_with_file
+
+# from pyCHX.chx_outlier_detection import (
+from chx_outlier_detection import is_outlier, outlier_mask
+
+# from pyCHX.chx_specklecp import (
+from chx_specklecp import (
+    get_binned_his_std,
+    get_contrast,
+    get_his_std_from_pds,
+    get_xsvs_fit,
+    plot_g2_contrast,
+    plot_xsvs_fit,
+    save_bin_his_std,
+    save_KM,
+    xsvsc,
+    xsvsp,
+)
+
+# from pyCH.chx_xpcs_xsvs_jupyter_V1 import(
+from chx_xpcs_xsvs_jupyter_V1 import (
+    compress_multi_uids,
+    do_compress_on_line,
+    get_fra_num_by_dose,
+    get_iq_from_uids,
+    get_series_g2_from_g12,
+    get_series_one_time_mulit_uids,
+    get_t_iqc_uids,
+    get_two_time_mulit_uids,
+    get_uids_by_range,
+    get_uids_in_time_period,
+    plot_dose_g2,
+    plot_entries_from_csvlist,
+    plot_entries_from_uids,
+    plot_t_iqc_uids,
+    plot_t_iqtMq2,
+    realtime_xpcs_analysis,
+    run_xpcs_xsvs_single,
+    wait_data_acquistion_finish,
+    wait_func,
+)
+
+# from pyCHX.Create_Report import (
+from Create_Report import (
+    create_multi_pdf_reports_for_uids,
+    create_one_pdf_reports_for_uids,
+    create_pdf_report,
+    export_xpcs_results_to_h5,
+    extract_xpcs_results_from_h5,
+    make_pdf_report,
+)
+
+# from pyCHX.DataGonio import qphiavg
+from DataGonio import qphiavg
+
+# from pyCHX.SAXS import (
+from SAXS import (
+    fit_form_factor,
+    fit_form_factor2,
+    form_factor_residuals_bg_lmfit,
+    form_factor_residuals_lmfit,
+    get_form_factor_fit_lmfit,
+    poly_sphere_form_factor_intensity,
+    show_saxs_qmap,
+)
+
+# from pyCHX.Two_Time_Correlation_Function import (
+from Two_Time_Correlation_Function import (
+    get_aged_g2_from_g12,
+    get_aged_g2_from_g12q,
+    get_four_time_from_two_time,
+    get_one_time_from_two_time,
+    rotate_g12q_to_rectangle,
+    show_C12,
+)
+
+# from pyCHX.XPCS_GiSAXS import (
+from XPCS_GiSAXS import (
+    cal_1d_qr,
+    convert_gisaxs_pixel_to_q,
+    fit_qr_qz_rate,
+    get_1d_qr,
+    get_each_box_mean_intensity,
+    get_gisaxs_roi,
+    get_qedge,
+    get_qmap_label,
+    get_qr_tick_label,
+    get_qzr_map,
+    get_qzrmap,
+    get_reflected_angles,
+    get_t_qrc,
+    multi_uids_gisaxs_xpcs_analysis,
+    plot_gisaxs_g4,
+    plot_gisaxs_two_g2,
+    plot_qr_1d_with_ROI,
+    plot_qrt_pds,
+    plot_qzr_map,
+    plot_t_qrc,
+    show_qzr_map,
+    show_qzr_roi,
+)
+
+# from pyCHX.XPCS_SAXS import (
+from XPCS_SAXS import (
+    cal_g2,
+    combine_two_roi_mask,
+    create_hot_pixel_mask,
+    get_angular_mask,
+    get_circular_average,
+    get_cirucular_average_std,
+    get_each_ring_mean_intensity,
+    get_QrQw_From_RoiMask,
+    get_ring_mask,
+    get_seg_from_ring_mask,
+    get_t_iq,
+    get_t_iqc,
+    multi_uids_saxs_xpcs_analysis,
+    plot_circular_average,
+    plot_qIq_with_ROI,
+    plot_t_iqc,
+    recover_img_from_iq,
+    save_lists,
+)

pyCHX/Badpixels.py

@@ -1,4 +1,5 @@
 """Dev@Octo12,2017"""
+
 import numpy as np
 
 damaged_4Mpixel = np.array(