diff --git a/dap/algos/addmask.py b/dap/algos/addmask.py index c1cc016..30799b8 100644 --- a/dap/algos/addmask.py +++ b/dap/algos/addmask.py @@ -1,6 +1,6 @@ #TODO: find a better way to handle this -def calc_apply_additional_mask(results, pixel_mask_pf): +def calc_apply_additional_mask(results, pixel_mask): apply_additional_mask = results.get("apply_additional_mask", False) if not apply_additional_mask: return @@ -11,64 +11,64 @@ def calc_apply_additional_mask(results, pixel_mask_pf): if detector_name == "JF06T08V07": # edge pixels - pixel_mask_pf[0:1030, 1100] = 0 - pixel_mask_pf[0:1030, 1613] = 0 - pixel_mask_pf[0:1030, 1650] = 0 + pixel_mask[0:1030, 1100] = 0 + pixel_mask[0:1030, 1613] = 0 + pixel_mask[0:1030, 1650] = 0 - pixel_mask_pf[67, 0:1063] = 0 + pixel_mask[67, 0:1063] = 0 - pixel_mask_pf[67:1097, 513] = 0 - pixel_mask_pf[67:1097, 550] = 0 - pixel_mask_pf[67:1097, 1063] = 0 + pixel_mask[67:1097, 513] = 0 + pixel_mask[67:1097, 550] = 0 + pixel_mask[67:1097, 1063] = 0 - pixel_mask_pf[1029, 1100:1614] = 0 - pixel_mask_pf[1029, 1650:2163] = 0 + pixel_mask[1029, 1100:1614] = 0 + pixel_mask[1029, 1650:2163] = 0 - pixel_mask_pf[1039, 1168:1682] = 0 - pixel_mask_pf[1039, 1718:2230] = 0 + pixel_mask[1039, 1168:1682] = 0 + pixel_mask[1039, 1718:2230] = 0 - pixel_mask_pf[1039:2069, 1168] = 0 - pixel_mask_pf[1039:2069, 1681] = 0 - pixel_mask_pf[1039:2069, 1718] = 0 + pixel_mask[1039:2069, 1168] = 0 + pixel_mask[1039:2069, 1681] = 0 + pixel_mask[1039:2069, 1718] = 0 - pixel_mask_pf[1096, 0:513] = 0 - pixel_mask_pf[1096, 550:1064] = 0 + pixel_mask[1096, 0:513] = 0 + pixel_mask[1096, 550:1064] = 0 - pixel_mask_pf[1106, 68:582] = 0 - pixel_mask_pf[1106, 618:1132] = 0 + pixel_mask[1106, 68:582] = 0 + pixel_mask[1106, 618:1132] = 0 - pixel_mask_pf[1106:2136, 581] = 0 - pixel_mask_pf[1106:2136, 618] = 0 - pixel_mask_pf[1106:2136, 1131] = 0 + pixel_mask[1106:2136, 581] = 0 + pixel_mask[1106:2136, 618] = 0 + pixel_mask[1106:2136, 1131] = 0 - pixel_mask_pf[2068, 1168:2232] = 0 + pixel_mask[2068, 1168:2232] = 0 # first bad region in left bottom inner module - pixel_mask_pf[842:1097, 669:671] = 0 + pixel_mask[842:1097, 669:671] = 0 # second bad region in left bottom inner module - pixel_mask_pf[1094, 620:807] = 0 + pixel_mask[1094, 620:807] = 0 # vertical line in upper left bottom module - pixel_mask_pf[842:1072, 87:90] = 0 + pixel_mask[842:1072, 87:90] = 0 # horizontal line? - pixel_mask_pf[1794, 1503:1550] = 0 + pixel_mask[1794, 1503:1550] = 0 # killed by CC - pixel_mask_pf[1499, 655:692] = 0 + pixel_mask[1499, 655:692] = 0 # module 12 right column - pixel_mask_pf[68:1096, 1062] = 0 + pixel_mask[68:1096, 1062] = 0 # module 16 left column - pixel_mask_pf[0:1028, 1101] = 0 + pixel_mask[0:1028, 1101] = 0 elif detector_name == "JF17T16V01": # mask module 11 - pixel_mask_pf[2619:3333,1577:2607] = 0 + pixel_mask[2619:3333,1577:2607] = 0 diff --git a/dap/algos/addmaskfile.py b/dap/algos/addmaskfile.py index f337f70..75ae67a 100644 --- a/dap/algos/addmaskfile.py +++ b/dap/algos/addmaskfile.py @@ -5,7 +5,7 @@ import numpy as np DEFAULT_MASK_DATASET = "mask_data" -def calc_apply_additional_mask_from_file(results, pixel_mask_pf): +def calc_apply_additional_mask_from_file(results, pixel_mask): apply_additional_mask = results.get("apply_additional_mask_from_file", False) if not apply_additional_mask: return @@ -31,6 +31,6 @@ def calc_apply_additional_mask_from_file(results, pixel_mask_pf): return try: - np.multiply(pixel_mask_pf, mask, out=pixel_mask_pf) + np.multiply(pixel_mask, mask, out=pixel_mask) except Exception as error: results["mask_error"] = f"Error applying additional mask from file {mask_file}:\n{error}" diff --git a/dap/algos/aggregation.py b/dap/algos/aggregation.py index 6281fbc..e6fcae9 100644 --- a/dap/algos/aggregation.py +++ b/dap/algos/aggregation.py @@ -2,14 +2,14 @@ from .mask import calc_mask_pixels from .thresh import threshold -def calc_apply_aggregation(results, data, pixel_mask_pf, aggregator): +def calc_apply_aggregation(results, data, pixel_mask, aggregator): # last round was ready, restart if aggregator.is_ready(): aggregator.reset() calc_apply_threshold(results, data) # changes data in place data = calc_aggregate(results, data, aggregator) - calc_mask_pixels(data, pixel_mask_pf) # changes data in place + calc_mask_pixels(data, pixel_mask) # changes data in place aggregator.nmax = results.get("aggregation_max") aggregation_is_ready = aggregator.is_ready() diff --git a/dap/algos/mask.py b/dap/algos/mask.py index 7ba422f..11e833b 100644 --- a/dap/algos/mask.py +++ b/dap/algos/mask.py @@ -1,11 +1,11 @@ import numpy as np -def calc_mask_pixels(data, pixel_mask_pf): - if pixel_mask_pf is None: +def calc_mask_pixels(data, pixel_mask): + if pixel_mask is None: return - data[~pixel_mask_pf] = np.nan + data[~pixel_mask] = np.nan diff --git a/dap/algos/peakfind.py b/dap/algos/peakfind.py index 6667d87..a706cb9 100644 --- a/dap/algos/peakfind.py +++ b/dap/algos/peakfind.py @@ -5,12 +5,12 @@ import numpy as np from peakfinder8_extension import peakfinder_8 -def calc_peakfinder_analysis(results, data, pixel_mask_pf): +def calc_peakfinder_analysis(results, data, pixel_mask): do_peakfinder_analysis = results.get("do_peakfinder_analysis", False) if not do_peakfinder_analysis: return - if pixel_mask_pf is None: + if pixel_mask is None: return for k in ("beam_center_x", "beam_center_y", "hitfinder_min_snr", "hitfinder_min_pix_count", "hitfinder_adc_thresh"): @@ -39,7 +39,7 @@ def calc_peakfinder_analysis(results, data, pixel_mask_pf): peak_list_x, peak_list_y, peak_list_value = peakfinder_8( max_num_peaks, data.astype(np.float32), - pixel_mask_pf.astype(np.int8), + pixel_mask.astype(np.int8), pix_r.astype(np.float32), asic_nx, asic_ny, nasics_x, nasics_y, diff --git a/dap/algos/radprof.py b/dap/algos/radprof.py index 42bc268..59fee1b 100644 --- a/dap/algos/radprof.py +++ b/dap/algos/radprof.py @@ -4,7 +4,7 @@ from .thresh import threshold from .utils import npmemo -def calc_radial_integration(results, data, pixel_mask_pf): +def calc_radial_integration(results, data, pixel_mask): do_radial_integration = results.get("do_radial_integration", False) if not do_radial_integration: return @@ -12,14 +12,14 @@ def calc_radial_integration(results, data, pixel_mask_pf): center_x = results["beam_center_x"] center_y = results["beam_center_y"] - rad, norm = prepare_radial_profile(data.shape, center_x, center_y, pixel_mask_pf) + rad, norm = prepare_radial_profile(data.shape, center_x, center_y, pixel_mask) r_min = min(rad) r_max = max(rad) + 1 data = calc_apply_threshold(results, data) - rp = radial_profile(data, rad, norm, pixel_mask_pf) + rp = radial_profile(data, rad, norm, pixel_mask) silent_min = results.get("radial_integration_silent_min", None) silent_max = results.get("radial_integration_silent_max", None) diff --git a/dap/worker.py b/dap/worker.py index cc18bff..895d4fd 100644 --- a/dap/worker.py +++ b/dap/worker.py @@ -105,32 +105,32 @@ def work(backend_addr, accumulator_addr, visualisation_addr, fn_config, skip_fra if image is None: continue - pixel_mask_pf = jfdata.get_pixel_mask(results, double_pixels) + pixel_mask = jfdata.get_pixel_mask(results, double_pixels) - if pixel_mask_pf is not None: + if pixel_mask is not None: saturated_pixels_y, saturated_pixels_x = jfdata.get_saturated_pixels(raw_image, double_pixels) results["saturated_pixels"] = len(saturated_pixels_x) results["saturated_pixels_x"] = saturated_pixels_x.tolist() results["saturated_pixels_y"] = saturated_pixels_y.tolist() - calc_radial_integration(results, image, pixel_mask_pf) + calc_radial_integration(results, image, pixel_mask) pfimage = image.copy() #TODO: is this copy needed? - calc_mask_pixels(pfimage, pixel_mask_pf) # changes pfimage in place + calc_mask_pixels(pfimage, pixel_mask) # changes pfimage in place calc_apply_threshold(results, pfimage) # changes pfimage in place - calc_roi(results, pfimage, pixel_mask_pf) + calc_roi(results, pfimage, pixel_mask) calc_spi_analysis(results, pfimage) - calc_peakfinder_analysis(results, pfimage, pixel_mask_pf) + calc_peakfinder_analysis(results, pfimage, pixel_mask) # ??? # Streak finder processing for convergent-beam diffraction experiments # changes image and mask in place if do_snr=True in parameters file - image = calc_streakfinder_analysis(results, image, pixel_mask_pf) + image = calc_streakfinder_analysis(results, image, pixel_mask) - image, aggregation_is_ready = calc_apply_aggregation(results, image, pixel_mask_pf, aggregator) + image, aggregation_is_ready = calc_apply_aggregation(results, image, pixel_mask, aggregator) results["type"] = str(image.dtype) results["shape"] = image.shape