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omit overlapping shoeboxes because we can't handle them yet #4

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omit overlapping shoeboxes because we can't handle them yet #4

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32 changes: 32 additions & 0 deletions adse13_187/adse13_221/basic_runner.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,10 @@
import math
from scipy import constants
ENERGY_CONV = 1e10*constants.c*constants.h / constants.electron_volt
REFL_BORDER = 3
SLOW_SIZE = 254
FAST_SIZE = 254
PANEL_SIZE = SLOW_SIZE * FAST_SIZE

class MCMC_manager:
def get_amplitudes(self, dials_model, refl_table, test_without_mpi=True):
Expand All @@ -32,6 +36,34 @@ def set_whitelist(self,value):
from LS49.adse13_187.adse13_221.lunus_wrap import mask_manager
class basic_run_manager(mask_manager):

def remove_overlaps(self):
refl = self.refl_table
pixels_irefls = dict()
irefls_noduplicates = flex.bool(refl.size(), True)
for i_refl in range(refl.size()):
pixels = []
bbox = refl[i_refl]['bbox']
panel = refl[i_refl]['panel']
slow_min = max(0, bbox[2]-REFL_BORDER)
slow_max = min(SLOW_SIZE, bbox[3]+REFL_BORDER)
fast_min = max(0, bbox[0]-REFL_BORDER)
fast_max = min(FAST_SIZE, bbox[1]+REFL_BORDER)

for i_slow in range(slow_min, slow_max):
for i_fast in range(fast_min, fast_max):
px = panel*PANEL_SIZE + i_slow*SLOW_SIZE + i_fast
pixels.append(px)

for px in pixels:
if px in pixels_irefls: #pixel in multiple shoeboxes
pixels_irefls[px].append(i_refl)
for i in pixels_irefls[px]:
irefls_noduplicates[i] = False
else:
pixels_irefls[px] = [i_refl]

self.refl_table = refl.select(irefls_noduplicates)

def refl_analysis(self,dials_model):
"""This function sets up some data structures (spots_*) allowing us to index into the spots
and pixels of interest. These will be repeatedly used during parameter refinement
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1 change: 1 addition & 0 deletions adse13_187/adse13_221/mcmc_runner.py
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Original file line number Diff line number Diff line change
Expand Up @@ -145,6 +145,7 @@ def parse_input():
def run(params):
basename = "%s_%05d."%(params.output.label, params.output.index)
M = mcmc_run_manager.from_files(params.trusted_mask, params.refl, params.expt)
M.remove_overlaps()
M.get_trusted_and_refl_mask()
M.refl_analysis(params.cryst) # new
M.simple_rmsd() # new
Expand Down