Fill XDS_template from base instead of writing 4 almost-identical files

MANIFEST.in

@@ -28,3 +28,4 @@ include src/instamatic/config/microscope/*.yaml
 include src/instamatic/config/scripts/*.md
 include src/instamatic/neural_network/*.p
 include src/instamatic/processing/PETS_input_keywords.csv
+include src/instamatic/processing/XDS_template.inp

src/instamatic/processing/ImgConversionDM.py

@@ -72,7 +72,7 @@ def __init__(
         self.name = 'DigitalMicrograph'
         self.method = method
 
-        from .XDS_templateDM import XDS_template
+        from .XDS_template import XDS_template_DM as XDS_template
 
         self.XDS_template = XDS_template
 

src/instamatic/processing/ImgConversionTPX.py

@@ -84,7 +84,7 @@ def __init__(
         self.name = 'TimePix_SU'
         self.method = method
 
-        from .XDS_templateTPX import XDS_template
+        from .XDS_template import XDS_template_TPX as XDS_template
 
         self.XDS_template = XDS_template
 

src/instamatic/processing/ImgConversionTVIPS.py

@@ -74,7 +74,7 @@ def __init__(
         self.name = 'TVIPS F416'
         self.method = method
 
-        from .XDS_templateTVIPS import XDS_template
+        from .XDS_template import XDS_template_TVIPS as XDS_template
 
         self.XDS_template = XDS_template
 

src/instamatic/processing/XDS_templateDM.py → src/instamatic/processing/XDS_template.inp

@@ -1,6 +1,4 @@
-from __future__ import annotations
-
-XDS_template = """! XDS.INP file for Rotation Electron Diffraction generated by `instamatic`
+! XDS.INP file for Rotation Electron Diffraction generated by `instamatic`
 ! {date}
 ! For definitions of input parameters, see:
 ! http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html
@@ -37,8 +35,8 @@
 STARTING_ANGLE= {starting_angle:0.4f}
 STARTING_FRAME= 1
 
-MAX_CELL_AXIS_ERROR=  0.03      !0.03 is default
-MAX_CELL_ANGLE_ERROR= 2.0       !2.0  is default
+MAX_CELL_AXIS_ERROR=  {max_cell_axis_error}      !0.03 is default
+MAX_CELL_ANGLE_ERROR= {max_cell_angle_error}       !2.0  is default
 
 TEST_RESOLUTION_RANGE=10. 1.0 !for calculation of Rmeas when analysing the intensity data for space group symmetry in the CORRECT step.
 !MIN_RFL_Rmeas=50             !50 is default - used in the CORRECT step for identification of possible space groups.
@@ -49,7 +47,7 @@
 NX={NX}     NY={NY}             !Number of pixels
 QX={QX:.4f}  QY={QY:.4f}          !Physical size of pixels (mm)
 OVERLOAD= 130000              !default value dependent on the detector used
-TRUSTED_REGION= 0.0  1.05   !default \"0.0 1.05\". Corners for square detector max \"0.0 1.4142\"
+TRUSTED_REGION= 0.0  1.05   !default "0.0 1.05". Corners for square detector max "0.0 1.4142"
 {untrusted_areas}
 {stretch_correction}
 SENSOR_THICKNESS=0.30
@@ -95,7 +93,7 @@
 
 !NBX=7  NBY=7            ! 3 is default, used to estimate the expected variation in a data image, see GAIN.cbf
 !BACKGROUND_PIXEL= 6.0   ! Background pixel belongs to background if variation less than given esds
-!STRONG_PIXEL= 3.0       ! Strong pixel must exceed background by more than number of given esds
+{strong_pixel_line}       ! Strong pixel must exceed background by more than number of given esds
 !MAXIMUM_NUMBER_OF_STRONG_PIXELS= 1500000 ! Approximate upper limit for the total number of 'strong' pixels
 !MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT= 6    ! Used to suppress spurious, isolated 'strong' pixels from entering the spot list
 !SPOT_MAXIMUM-CENTROID= 3.0               ! Maximum deviation of spot maximum from spot centroid
@@ -109,10 +107,9 @@
 
 ! ********** Indexing **********
 
-MINIMUM_FRACTION_OF_INDEXED_SPOTS= 0.25    ! 0.50 is default.
+{min_fraction_line}    !0.50 is default.
 !MAXIMUM_ERROR_OF_SPOT_POSITION=6.0        ! 3.0 is default
 !REFLECTING_RANGE=
 !REFLECTING_RANGE_E.S.D.=
 !BEAM_DIVERGENCE=
 !BEAM_DIVERGENCE_E.S.D.=
-"""

src/instamatic/processing/XDS_template.py

@@ -1,118 +1,30 @@
 from __future__ import annotations
 
-XDS_template = """! XDS.INP file for Rotation Electron Diffraction generated by `instamatic`
-! {date}
-! For definitions of input parameters, see:
-! http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html
-!
-! cRED implementation reference paper:
-! J. Appl. Cryst. (2018). 51, 1652–1661. http://dx.doi.org/10.1107/S1600576718015145
+from dataclasses import asdict, dataclass
+from importlib.resources import files
 
-! ********** Job control **********
+from instamatic._collections import PartialFormatter
 
-!JOB= XYCORR INIT COLSPOT IDXREF
-!JOB= DEFPIX INTEGRATE CORRECT
-!JOB= CORRECT
+XDS_template_path = files('instamatic.processing').joinpath('XDS_template.inp')
+XDS_template_base = XDS_template_path.read_text(encoding='utf-8')
 
-MAXIMUM_NUMBER_OF_JOBS=4
-MAXIMUM_NUMBER_OF_PROCESSORS=4
 
-! ********** Data images **********
+@dataclass
+class XDSPreset:
+    max_cell_axis_error: str = '0.05'
+    max_cell_angle_error: str = '3.0'
+    strong_pixel_line: str = '!STRONG_PIXEL= 3.0'
+    min_fraction_line: str = '!MINIMUM_FRACTION_OF_INDEXED_SPOTS= 0.25'
 
-NAME_TEMPLATE_OF_DATA_FRAMES= {data_drc}/0????.img   SMV
-DATA_RANGE=           {data_begin:d} {data_end:d}
-SPOT_RANGE=           {data_begin:d} {data_end:d}
-BACKGROUND_RANGE=     {data_begin:d} {data_end:d}
-{exclude:s}
 
-! ********** Crystal **********
+mce = {'max_cell_axis_error': '0.03', 'max_cell_angle_error': '2.0'}
 
-!SPACE_GROUP_NUMBER= 0
-!UNIT_CELL_CONSTANTS= 10 20 30 90 90 90
+xds_preset_base = XDSPreset()
+xds_preset_dm = XDSPreset(min_fraction_line='MINIMUM_FRACTION_OF_INDEXED_SPOTS= 0.25 ', **mce)
+xds_preset_tvips = XDSPreset(strong_pixel_line='STRONG_PIXEL= 6.0 ', **mce)
 
-!REIDX=                       !Optional reindexing transformation to apply on reflection indices
-FRIEDEL'S_LAW=TRUE            !TRUE is default
-
-!phi(i) = STARTING_ANGLE + OSCILLATION_RANGE * (i - STARTING_FRAME)
-STARTING_ANGLE= {starting_angle:0.4f}
-STARTING_FRAME= 1
-
-MAX_CELL_AXIS_ERROR=  0.05      !0.03 is default
-MAX_CELL_ANGLE_ERROR= 3.0       !2.0  is default
-
-TEST_RESOLUTION_RANGE=10. 1.0 !for calculation of Rmeas when analysing the intensity data for space group symmetry in the CORRECT step.
-!MIN_RFL_Rmeas=50             !50 is default - used in the CORRECT step for identification of possible space groups.
-!MAX_FAC_Rmeas=2.0            !2.0 is default - used in the CORRECT step for identification of possible space groups.
-
-! ********** Detector hardware **********
-
-NX={NX}     NY={NY}             !Number of pixels
-QX={QX:.4f}  QY={QY:.4f}          !Physical size of pixels (mm)
-OVERLOAD= 130000              !default value dependent on the detector used
-TRUSTED_REGION= 0.0  1.05   !default \"0.0 1.05\". Corners for square detector max \"0.0 1.4142\"
-{untrusted_areas}
-{stretch_correction}
-SENSOR_THICKNESS=0.30
-AIR=0.0
-
-! ********** Trusted detector region **********
-
-VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS= 10 30000 !Values are defined in `ABS.CBF`, check mask in `BKGPIX.CBF`, used in DEFPIX
-!MINIMUM_ZETA=                                    !0.05 is default
-
-INCLUDE_RESOLUTION_RANGE= 20 0.8
-
-!Ice Ring exclusion, important for data collected using cryo holders
-!EXCLUDE_RESOLUTION_RANGE= 3.93 3.87       !ice-ring at 3.897 Angstrom
-!EXCLUDE_RESOLUTION_RANGE= 3.70 3.64       !ice-ring at 3.669 Angstrom
-!EXCLUDE_RESOLUTION_RANGE= 3.47 3.41       !ice-ring at 3.441 Angstrom (Main)
-!EXCLUDE_RESOLUTION_RANGE= 2.70 2.64       !ice-ring at 2.671 Angstrom
-!EXCLUDE_RESOLUTION_RANGE= 2.28 2.22       !ice-ring at 2.249 Angstrom (Main)
-!EXCLUDE_RESOLUTION_RANGE= 2.102 2.042     !ice-ring at 2.072 Angstrom - strong
-!EXCLUDE_RESOLUTION_RANGE= 1.978 1.918     !ice-ring at 1.948 Angstrom - weak
-!EXCLUDE_RESOLUTION_RANGE= 1.948 1.888     !ice-ring at 1.918 Angstrom - strong
-!EXCLUDE_RESOLUTION_RANGE= 1.913 1.853     !ice-ring at 1.883 Angstrom - weak
-!EXCLUDE_RESOLUTION_RANGE= 1.751 1.691     !ice-ring at 1.721 Angstrom - weak
-
-! ********** Detector geometry & Rotation axis **********
-
-DIRECTION_OF_DETECTOR_X-AXIS= 1 0 0
-DIRECTION_OF_DETECTOR_Y-AXIS= 0 1 0
-
-ORGX= {origin_x:.2f}    ORGY= {origin_y:.2f}           !Detector origin (pixels). Often close to the image center, i.e. ORGX=NX/2; ORGY=NY/2
-DETECTOR_DISTANCE= {sign}{detector_distance:.2f}            !Can be negative. Positive because the detector normal points away from the crystal.
-
-OSCILLATION_RANGE= {osc_angle:.4f}
-
-ROTATION_AXIS= {rot_x:.4f} {rot_y:.4f} {rot_z:.4f}
-
-! ********** Incident beam **********
-
-X-RAY_WAVELENGTH= {wavelength:.4f}              !used by IDXREF
-INCIDENT_BEAM_DIRECTION= 0 0 1        !The vector points from the source towards the crystal
-
-! ********** Background and peak pixels **********
-
-!NBX=7  NBY=7            ! 3 is default, used to estimate the expected variation in a data image, see GAIN.cbf
-!BACKGROUND_PIXEL= 6.0   ! Background pixel belongs to background if variation less than given esds
-!STRONG_PIXEL= 3.0       ! Strong pixel must exceed background by more than number of given esds
-!MAXIMUM_NUMBER_OF_STRONG_PIXELS= 1500000 ! Approximate upper limit for the total number of 'strong' pixels
-!MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT= 6    ! Used to suppress spurious, isolated 'strong' pixels from entering the spot list
-!SPOT_MAXIMUM-CENTROID= 3.0               ! Maximum deviation of spot maximum from spot centroid
-!SIGNAL_PIXEL= 3.0                        ! Signal pixels must exceed background by more than given esds
-
-! ********** Refinement **********
-
- REFINE(IDXREF)=    BEAM AXIS ORIENTATION CELL !POSITION
- REFINE(INTEGRATE)= !POSITION BEAM AXIS !ORIENTATION CELL
- REFINE(CORRECT)=   BEAM AXIS ORIENTATION CELL !POSITION
-
-! ********** Indexing **********
-
-!MINIMUM_FRACTION_OF_INDEXED_SPOTS= 0.25    !0.50 is default.
-!MAXIMUM_ERROR_OF_SPOT_POSITION=6.0        ! 3.0 is default
-!REFLECTING_RANGE=
-!REFLECTING_RANGE_E.S.D.=
-!BEAM_DIVERGENCE=
-!BEAM_DIVERGENCE_E.S.D.=
-"""
+pf = PartialFormatter()
+XDS_template = pf.format(XDS_template_base, **asdict(xds_preset_base))
+XDS_template_DM = pf.format(XDS_template_base, **asdict(xds_preset_dm))
+XDS_template_TPX = XDS_template
+XDS_template_TVIPS = pf.format(XDS_template_base, **asdict(xds_preset_tvips))