Add a point background model to TOF (#41)

* Bump from 0.9.2 to 0.9.3 (#38) * Fix summary (#34) * Modify summary page * Add measured and processed data for TOF * Move report.cif from Analysis main view to sidebar text mode * Show html-based analysis summary in the Analysis main view * Allow saving analysis summary as html * Update images for GUI tests * Fix signing macos (#35) * Temporarily remove the CI script for snapcraft * Simplify build script to try code signing * MACOS_CERTIFICATE_ENCODED (.p12 content base64 encoded) updated on github * MACOS_CERTIFICATE_PASSWORD (.p12 password) updated on github * Rename fpath to fname * Migrate from altool to notarytool * altool is depricated * Migration instruction https://developer.apple.com/documentation/technotes/tn3147-migrating-to-the-latest-notarization-tool * Fix spctl verbose output option * Try using lando/code-sign-action instead of custom script * Fix file path in the code signing script * Update certificate identity * Debug * Fix identity * more debug * more debug * more debug * more debug * debug: return after verify * debug: return after sign * debug: return before verify * debug 2: return after sign * more debug * Another try with lando/code-sign-action * More debug terminal * more debug * fix * More fixes * More fixes * continue after signing * Remove sleep before staple (moved to notarisation) * clean up * Rename variables and clean up * More clean up * Fix team-id * Restore other steps in the build script * Force to use numpy<2 * Use full os name in uploaded artifacts * Windows signing (#33) * initial test, mostly to get the filenames first * attempt to locate the signed binary * play with filename * try again * another attempt at properly delimit the string * go back to the whole matrix before PR * remove debug printouts * Get path to setup_exe from Config.py --------- Co-authored-by: Andrew Sazonov <andrew.sazonov@icloud.com> * Prepare for releasing 0.9.2 * Fix release info [ci skip] * Return snapcraft build script back (#37) * Update release info --------- Co-authored-by: Piotr Rozyczko <piotr.rozyczko@gmail.com> * Bump from v0.9.2 to v0.9.3 (#39) * Fix summary (#34) * Modify summary page * Add measured and processed data for TOF * Move report.cif from Analysis main view to sidebar text mode * Show html-based analysis summary in the Analysis main view * Allow saving analysis summary as html * Update images for GUI tests * Fix signing macos (#35) * Temporarily remove the CI script for snapcraft * Simplify build script to try code signing * MACOS_CERTIFICATE_ENCODED (.p12 content base64 encoded) updated on github * MACOS_CERTIFICATE_PASSWORD (.p12 password) updated on github * Rename fpath to fname * Migrate from altool to notarytool * altool is depricated * Migration instruction https://developer.apple.com/documentation/technotes/tn3147-migrating-to-the-latest-notarization-tool * Fix spctl verbose output option * Try using lando/code-sign-action instead of custom script * Fix file path in the code signing script * Update certificate identity * Debug * Fix identity * more debug * more debug * more debug * more debug * debug: return after verify * debug: return after sign * debug: return before verify * debug 2: return after sign * more debug * Another try with lando/code-sign-action * More debug terminal * more debug * fix * More fixes * More fixes * continue after signing * Remove sleep before staple (moved to notarisation) * clean up * Rename variables and clean up * More clean up * Fix team-id * Restore other steps in the build script * Force to use numpy<2 * Use full os name in uploaded artifacts * Windows signing (#33) * initial test, mostly to get the filenames first * attempt to locate the signed binary * play with filename * try again * another attempt at properly delimit the string * go back to the whole matrix before PR * remove debug printouts * Get path to setup_exe from Config.py --------- Co-authored-by: Andrew Sazonov <andrew.sazonov@icloud.com> * Prepare for releasing 0.9.2 * Fix release info [ci skip] * Return snapcraft build script back (#37) * Update release info --------- Co-authored-by: Piotr Rozyczko <piotr.rozyczko@gmail.com> * Bump from v0.9.2 to v0.9.3 (#40) * Fix summary (#34) * Modify summary page * Add measured and processed data for TOF * Move report.cif from Analysis main view to sidebar text mode * Show html-based analysis summary in the Analysis main view * Allow saving analysis summary as html * Update images for GUI tests * Fix signing macos (#35) * Temporarily remove the CI script for snapcraft * Simplify build script to try code signing * MACOS_CERTIFICATE_ENCODED (.p12 content base64 encoded) updated on github * MACOS_CERTIFICATE_PASSWORD (.p12 password) updated on github * Rename fpath to fname * Migrate from altool to notarytool * altool is depricated * Migration instruction https://developer.apple.com/documentation/technotes/tn3147-migrating-to-the-latest-notarization-tool * Fix spctl verbose output option * Try using lando/code-sign-action instead of custom script * Fix file path in the code signing script * Update certificate identity * Debug * Fix identity * more debug * more debug * more debug * more debug * debug: return after verify * debug: return after sign * debug: return before verify * debug 2: return after sign * more debug * Another try with lando/code-sign-action * More debug terminal * more debug * fix * More fixes * More fixes * continue after signing * Remove sleep before staple (moved to notarisation) * clean up * Rename variables and clean up * More clean up * Fix team-id * Restore other steps in the build script * Force to use numpy<2 * Use full os name in uploaded artifacts * Windows signing (#33) * initial test, mostly to get the filenames first * attempt to locate the signed binary * play with filename * try again * another attempt at properly delimit the string * go back to the whole matrix before PR * remove debug printouts * Get path to setup_exe from Config.py --------- Co-authored-by: Andrew Sazonov <andrew.sazonov@icloud.com> * Prepare for releasing 0.9.2 * Fix release info * Return snapcraft build script back (#37) * Update release info --------- Co-authored-by: Piotr Rozyczko <piotr.rozyczko@gmail.com> * Initial implementation of point background for TOF * Clean up debugging * Force scipy<1.14 --------- Co-authored-by: Piotr Rozyczko <piotr.rozyczko@gmail.com>
EasyScience · Jun 26, 2024 · 88b962a · 88b962a
1 parent a92ed72
commit 88b962a
Show file tree

Hide file tree

Showing 14 changed files with 202 additions and 135 deletions.
diff --git a/easyDiffractionApp/Examples/CeCuAl3_Polaris@ISIS/experiments/polaris.cif b/easyDiffractionApp/Examples/CeCuAl3_Polaris@ISIS/experiments/polaris.cif
@@ -11,27 +11,26 @@ _pd_instr.beta1 0.00224
 _pd_instr.sigma0 0.409
 _pd_instr.sigma1 8.118
 
-_tof_background.coeff1 25101(108)
-_tof_background.coeff2 6940(199)
-_tof_background.coeff3 8460(189)
-_tof_background.coeff4 3452(162)
-_tof_background.coeff5 2812(157)
-_tof_background.coeff6 545(122)
-_tof_background.coeff7 1000(128)
-_tof_background.coeff8 9(77)
-_tof_background.coeff9 116(78)
-_tof_background.coeff10 0.0
-_tof_background.coeff11 0.0
-_tof_background.coeff12 0.0
-_tof_background.coeff13 0.0
-_tof_background.coeff14 0.0
-_tof_background.coeff15 0.0
-_tof_background.coeff16 0.0
-_tof_background.coeff17 0.0
-_tof_background.coeff18 0.0
-
 _diffrn_radiation.probe neutron
 
+loop_
+_pd_background.line_segment_X
+_pd_background.line_segment_intensity
+_pd_background.X_coordinate
+3000.0 33469(55) time-of-flight
+4000.0 27344(46) time-of-flight
+5000.0 23749(54) time-of-flight
+6000.0 20995(65) time-of-flight
+7000.0 19795(71) time-of-flight
+9000.0 18381(91) time-of-flight
+11000.0 18983(136) time-of-flight
+13000.0 20745(237) time-of-flight
+15000.0 19626(352) time-of-flight
+16000.0 22778(634) time-of-flight
+17000.0 23899(837) time-of-flight
+18000.0 25356(985) time-of-flight
+19000.0 25188(1649) time-of-flight
+
 loop_
 _pd_phase_block.id
 _pd_phase_block.scale
@@ -3733,4 +3732,4 @@ _pd_meas.intensity_total_su
 18976.191 26208.0 5806.0
 18985.67 19929.0 5494.0
 18995.164 26780.0 5848.0
-19004.658 22232.0 5634.0
+19004.658 22232.0 5634.0
diff --git a/easyDiffractionApp/Examples/Na2Ca3Al2F14_Osiris@ISIS/experiments/osiris.cif b/easyDiffractionApp/Examples/Na2Ca3Al2F14_Osiris@ISIS/experiments/osiris.cif
@@ -5,33 +5,34 @@ _pd_instr.dtt1 17591.139
 _pd_instr.dtt2 -0.56(5)
 _pd_instr.zero 2.4(2)
 _pd_instr.alpha0 0.0
-_pd_instr.alpha1 0.0773(9)
-_pd_instr.beta0 0.01079(7)
+_pd_instr.alpha1 0.0772(9)
+_pd_instr.beta0 0.01078(7)
 _pd_instr.beta1 0.0555(9)
 _pd_instr.sigma0 0.0
 _pd_instr.sigma1 13.2(1)
 
-_tof_background.coeff1 819(43)
-_tof_background.coeff2 737(85)
-_tof_background.coeff3 717(83)
-_tof_background.coeff4 567(79)
-_tof_background.coeff5 441(74)
-_tof_background.coeff6 316(68)
-_tof_background.coeff7 230(61)
-_tof_background.coeff8 157(54)
-_tof_background.coeff9 102(46)
-_tof_background.coeff10 58(39)
-_tof_background.coeff11 20(32)
-_tof_background.coeff12 -3(25)
-_tof_background.coeff13 -19(19)
-_tof_background.coeff14 -19(14)
-_tof_background.coeff15 -20(10)
-_tof_background.coeff16 -8(7)
-_tof_background.coeff17 -9(4)
-_tof_background.coeff18 -5(3)
-
 _diffrn_radiation.probe neutron
 
+loop_
+_pd_background.line_segment_X
+_pd_background.line_segment_intensity
+_pd_background.X_coordinate
+14918.0 1915(55) time-of-flight
+16000.0 1661(28) time-of-flight
+18000.0 1511(17) time-of-flight
+20000.0 1059(12) time-of-flight
+22000.0 885(8) time-of-flight
+25000.0 758(6) time-of-flight
+30000.0 607(5) time-of-flight
+35000.0 523(4) time-of-flight
+40000.0 416(3) time-of-flight
+50000.0 363(3) time-of-flight
+70000.0 394(3) time-of-flight
+90000.0 425(6) time-of-flight
+110000.0 445(10) time-of-flight
+120000.0 484(14) time-of-flight
+135002.0 487(10) time-of-flight
+
 loop_
 _pd_phase_block.id
 _pd_phase_block.scale

diff --git a/easyDiffractionApp/Examples/Na2Ca3Al2F14_WISH@ISIS/experiments/wish.cif b/easyDiffractionApp/Examples/Na2Ca3Al2F14_WISH@ISIS/experiments/wish.cif
@@ -1,41 +1,55 @@
 data_wish
 
 _pd_instr.2theta_bank 152.827
-_pd_instr.dtt1 20773.9(3)
+_pd_instr.dtt1 20773.5(3)
 _pd_instr.dtt2 -1.08308
-_pd_instr.zero -15.0(5)
-_pd_instr.alpha0 -0.0160(8)
-_pd_instr.alpha1 0.121(3)
-_pd_instr.beta0 0.00663(3)
-_pd_instr.beta1 0.0100(3)
+_pd_instr.zero -14.4(5)
+_pd_instr.alpha0 -0.0162(8)
+_pd_instr.alpha1 0.122(3)
+_pd_instr.beta0 0.00658(3)
+_pd_instr.beta1 0.0108(3)
 _pd_instr.sigma0 0.0
 _pd_instr.sigma1 7.5(2)
 
-_tof_background.coeff1 307(16)
-_tof_background.coeff2 63(32)
-_tof_background.coeff3 18(31)
-_tof_background.coeff4 -27(30)
-_tof_background.coeff5 -45(29)
-_tof_background.coeff6 -45(27)
-_tof_background.coeff7 -46(25)
-_tof_background.coeff8 -45(23)
-_tof_background.coeff9 -40(20)
-_tof_background.coeff10 -31(17)
-_tof_background.coeff11 -23(15)
-_tof_background.coeff12 -21(12)
-_tof_background.coeff13 -16(10)
-_tof_background.coeff14 -11(8)
-_tof_background.coeff15 -5(6)
-_tof_background.coeff16 -3(4)
-_tof_background.coeff17 1(2)
-_tof_background.coeff18 -2(2)
-
 _diffrn_radiation.probe neutron
 
+loop_
+_pd_background.line_segment_X
+_pd_background.line_segment_intensity
+_pd_background.X_coordinate
+9162.304 466(39) time-of-flight
+11136.874 593(30) time-of-flight
+13313.388 497(22) time-of-flight
+14906.508 546(19) time-of-flight
+16454.75 533(17) time-of-flight
+17352.281 497(14) time-of-flight
+18743.455 429(10) time-of-flight
+20179.508 453(10) time-of-flight
+21368.736 397(9) time-of-flight
+22176.04 473(12) time-of-flight
+22827.227 478(9) time-of-flight
+24644.729 380(6) time-of-flight
+26439.791 381(5) time-of-flight
+28257.293 378(5) time-of-flight
+31196.71 343(4) time-of-flight
+34034.406 328(4) time-of-flight
+37265.52 309(4) time-of-flight
+41214.66 322(3) time-of-flight
+44827.227 282(3) time-of-flight
+49830.965 272(4) time-of-flight
+52905.01 257(4) time-of-flight
+58204.938 260(4) time-of-flight
+62916.98 261(4) time-of-flight
+70186.984 262(5) time-of-flight
+74204.94 262(6) time-of-flight
+82103.22 268(6) time-of-flight
+91958.87 268(7) time-of-flight
+102712.04 262(15) time-of-flight
+
 loop_
 _pd_phase_block.id
 _pd_phase_block.scale
-ncaf 1.087(5)
+ncaf 1.095(5)
 
 loop_
 _pd_meas.time_of_flight

diff --git a/easyDiffractionApp/Examples/Si_SEPD@Argonne/experiments/sepd.cif b/easyDiffractionApp/Examples/Si_SEPD@Argonne/experiments/sepd.cif
@@ -1,41 +1,37 @@
 data_sepd
 
+_diffrn_radiation.probe neutron
+
 _pd_instr.2theta_bank 144.845
 _pd_instr.dtt1 7476.91
 _pd_instr.dtt2 -1.54
-_pd_instr.zero -9.26(5)
+_pd_instr.zero -9.24(5)
 _pd_instr.alpha0 0.0
 _pd_instr.alpha1 0.5971
 _pd_instr.beta0 0.04221
 _pd_instr.beta1 0.00946
-_pd_instr.sigma0 0.21(6)
-_pd_instr.sigma1 7.08(6)
-
-_tof_background.coeff1 154.8(6)
-_tof_background.coeff2 1(1)
-_tof_background.coeff3 36.8(9)
-_tof_background.coeff4 12.1(8)
-_tof_background.coeff5 17.7(8)
-_tof_background.coeff6 5.0(7)
-_tof_background.coeff7 6.8(5)
-_tof_background.coeff8 0.0
-_tof_background.coeff9 0.0
-_tof_background.coeff10 0.0
-_tof_background.coeff11 0.0
-_tof_background.coeff12 0.0
-_tof_background.coeff13 0.0
-_tof_background.coeff14 0.0
-_tof_background.coeff15 0.0
-_tof_background.coeff16 0.0
-_tof_background.coeff17 0.0
-_tof_background.coeff18 0.0
+_pd_instr.sigma0 0.30(6)
+_pd_instr.sigma1 7.01(6)
 
-_diffrn_radiation.probe neutron
+loop_
+_pd_background.line_segment_X
+_pd_background.line_segment_intensity
+_pd_background.X_coordinate
+2000.0 221.1 time-of-flight
+4000.0 169.5 time-of-flight
+6000.0 135.4 time-of-flight
+10000.0 121.4 time-of-flight
+14000.0 132.2 time-of-flight
+18000.0 134 time-of-flight
+22000.0 143 time-of-flight
+25000.0 183 time-of-flight
+28000.0 165 time-of-flight
+29995.0 204 time-of-flight
 
 loop_
 _pd_phase_block.id
 _pd_phase_block.scale
-si 15.01(4)
+si 14.97(4)
 
 loop_
 _pd_meas.time_of_flight

diff --git a/easyDiffractionApp/Gui/Components/Pages/Experiment/SideBarBasic.qml b/easyDiffractionApp/Gui/Components/Pages/Experiment/SideBarBasic.qml
@@ -135,13 +135,14 @@ EaComponents.SideBarColumn {
                 if (JSON.stringify(Globals.Proxies.experimentMainParam('_diffrn_radiation', 'type')) === '{}') {
                     return ''
                 }
-                if (Globals.Proxies.experimentMainParam('_diffrn_radiation', 'type').value === 'cwl') {
-                    return 'SideBarBasic/PdBackground.qml'
-                } else if (Globals.Proxies.experimentMainParam('_diffrn_radiation', 'type').value === 'tof') {
-                    return 'SideBarBasic/PdBackground_TOF.qml'
-                } else {
-                    return ''
-                }
+                //if (Globals.Proxies.experimentMainParam('_diffrn_radiation', 'type').value === 'cwl') {
+                //    return 'SideBarBasic/PdBackground.qml'
+                //} else if (Globals.Proxies.experimentMainParam('_diffrn_radiation', 'type').value === 'tof') {
+                //    return 'SideBarBasic/PdBackground_TOF.qml'
+                //} else {
+                //    return ''
+                //}
+                return 'SideBarBasic/PdBackground.qml'
             }
         }
     }

diff --git a/easyDiffractionApp/Gui/Globals/Configs.qml b/easyDiffractionApp/Gui/Globals/Configs.qml
@@ -25,7 +25,7 @@ QtObject { // If "Unknown component. (M300) in QtCreator", try: "Tools > QML/JS
                     readonly property string branch_url: ''
                     readonly property string commit_sha_short: ''
                     readonly property string commit_url: ''
-                    readonly property string build_date: '29 May 2024'
+                    readonly property string build_date: '21 Jun 2024'
                 }
             }
         }

diff --git a/easyDiffractionApp/Logic/Calculators.py b/easyDiffractionApp/Logic/Calculators.py
@@ -14,7 +14,7 @@
         str_to_globaln
     from cryspy.A_functions_base.function_2_space_group import \
         get_it_coordinate_system_codes_by_it_number
-    console.debug('CrysPy module imported')
+    #console.debug('CrysPy module imported')
 except ImportError:
     console.error('No CrysPy module found')
 
@@ -237,6 +237,8 @@ def edCifToCryspyCif(edCif, diffrn_radiation_type='cwl'):
             # NEED to remove this and use our handling of a background as for TOF case
             '_pd_background.line_segment_X': '_pd_background_2theta',
             '_pd_background.line_segment_intensity': '_pd_background_intensity',
+            '_pd_background.X_coordinate': '_pd_background_X_coordinate',
+
         }
         edToCryspyNamesMap['tof'] = {
             '_pd_instr.zero': '_tof_parameters_Zero',
@@ -256,8 +258,12 @@ def edCifToCryspyCif(edCif, diffrn_radiation_type='cwl'):
             '_pd_instr.sigma1': '_tof_profile_sigma1',
             '_pd_instr.sigma2': '_tof_profile_sigma2',
 
-            '_tof_background.time_max': '_tof_background_time_max',
-            '_tof_background.coeff': '_tof_background_coeff',
+            ###'_tof_background.time_max': '_tof_background_time_max',
+            ###'_tof_background.coeff': '_tof_background_coeff',
+
+            '_pd_background.line_segment_X': '_tof_backgroundpoint_time',
+            '_pd_background.line_segment_intensity': '_tof_backgroundpoint_intensity',
+            '_pd_background.X_coordinate': '_tof_backgroundpoint.X_coordinate',
 
             '_pd_meas.time_of_flight': '_tof_meas_time',
             '_pd_meas.intensity_total_su': '_tof_meas_intensity_sigma',  # before _pd_meas.intensity_total!
@@ -1251,14 +1257,14 @@ def cryspyObjAndDictToEdExperiments(cryspy_obj, cryspy_dict):  # NEED to be modi
                             #    fit = item.gamma2_refinement
                             #))
 
-                    # Ed (pycifstar processed) background section
-                    elif type(item) is cryspy.B_parent_classes.cl_2_loop.LoopN and item.items[0].PREFIX == 'pd_background':
-                        pycifstar_bkg_points = item.items
+                    # Cryspy background section (TOF, points)
+                    elif type(item) is cryspy.C_item_loop_classes.cl_1_tof_background_by_points.TOFBackgroundPointL:
+                        cryspy_bkg_points = item.items
                         ed_bkg_points = []
-                        for idx, pycifstar_bkg_point in enumerate(pycifstar_bkg_points):
+                        for idx, cryspy_bkg_point in enumerate(cryspy_bkg_points):
                             ed_bkg_point = {}
                             ed_bkg_point['line_segment_X'] = dict(Parameter(
-                                pycifstar_bkg_point.line_segment_x,
+                                cryspy_bkg_point.time,
                                 idx = idx,
                                 category = '_pd_background',
                                 name = 'line_segment_X',
@@ -1268,13 +1274,12 @@ def cryspyObjAndDictToEdExperiments(cryspy_obj, cryspy_dict):  # NEED to be modi
                                 cifDict = 'pd'
                             ))
                             ed_bkg_point['line_segment_intensity'] = dict(Parameter(
-                                pycifstar_bkg_point.line_segment_intensity,
-                                #error = pycifstar_bkg_point.line_segment_intensity_sigma,
-                                error = 1.0,
+                                cryspy_bkg_point.intensity,
+                                error = cryspy_bkg_point.intensity_sigma,
                                 idx = idx,
                                 category = '_pd_background',
                                 prettyCategory = 'bkg',
-                                rowName = f'{pycifstar_bkg_point.line_segment_x:g}µs',  # formatting float to str without trailing zeros
+                                rowName = f'{cryspy_bkg_point.time:g}µs',  # formatting float to str without trailing zeros
                                 name = 'line_segment_intensity',
                                 prettyName = 'intensity',
                                 shortPrettyName = 'Ibkg',
@@ -1284,7 +1289,7 @@ def cryspyObjAndDictToEdExperiments(cryspy_obj, cryspy_dict):  # NEED to be modi
                                 cifDict = 'pd',
                                 pctDelta = 25,
                                 fittable = True,
-                                fit = pycifstar_bkg_point.line_segment_intensity_refinement
+                                fit = cryspy_bkg_point.intensity_refinement
                             ))
                             ed_bkg_point['X_coordinate'] = dict(Parameter(
                                 'time-of-flight',
@@ -1299,7 +1304,7 @@ def cryspyObjAndDictToEdExperiments(cryspy_obj, cryspy_dict):  # NEED to be modi
                             ed_bkg_points.append(ed_bkg_point)
                         ed_experiment_no_meas['loops']['_pd_background'] = ed_bkg_points
 
-                    # Cryspy background section (TOF, polinom coeffs?)
+                    # Cryspy background section (TOF, polinom coeffs)
                     elif type(item) is cryspy.C_item_loop_classes.cl_1_tof_background.TOFBackground:
                         if hasattr(item, 'time_max'):
                             if not '_tof_background' in ed_experiment_no_meas['params']:

diff --git a/easyDiffractionApp/Logic/Data.py b/easyDiffractionApp/Logic/Data.py
@@ -10,7 +10,7 @@
 try:
     from cryspy.H_functions_global.function_1_cryspy_objects import \
         str_to_globaln
-    console.debug('CrysPy module imported')
+    #console.debug('CrysPy module imported')
 except ImportError:
     console.error('No CrysPy module found')