Skip to content
GitLab
Explore
Sign in
Primary navigation
Search or go to…
Project
S
Scipt base
Manage
Activity
Members
Labels
Plan
Issues
Issue boards
Milestones
Iterations
Wiki
Requirements
Code
Merge requests
Repository
Branches
Commits
Tags
Repository graph
Compare revisions
Snippets
Locked files
Build
Pipelines
Jobs
Pipeline schedules
Test cases
Artifacts
Deploy
Releases
Package registry
Container registry
Model registry
Operate
Environments
Terraform modules
Monitor
Incidents
Analyze
Value stream analytics
Contributor analytics
CI/CD analytics
Repository analytics
Code review analytics
Issue analytics
Insights
Model experiments
Help
Help
Support
GitLab documentation
Compare GitLab plans
Community forum
Contribute to GitLab
Provide feedback
Terms and privacy
Keyboard shortcuts
?
Snippets
Groups
Projects
Show more breadcrumbs
Koziej Lab
X-ray Diffraction
PDF
FlyPDF
Scipt base
Commits
b1620a25
Commit
b1620a25
authored
1 month ago
by
Gröne, Tjark Leon Raphael
Browse files
Options
Downloads
Patches
Plain Diff
Update file PDF_generator.py
parent
e1797d4b
Branches
Branches containing commit
No related tags found
No related merge requests found
Changes
1
Hide whitespace changes
Inline
Side-by-side
Showing
1 changed file
pure code not instalable as environment/PDF_generator.py
+5
-31
5 additions, 31 deletions
pure code not instalable as environment/PDF_generator.py
with
5 additions
and
31 deletions
pure code not instalable as environment/PDF_generator.py
+
5
−
31
View file @
b1620a25
...
...
@@ -122,15 +122,14 @@ endScan = bg.platoend_index
# Save the files for the BG subtration as .dat
bg
.
outputDatFile
(
rootdir
+
'
/processed/
'
+
meas_sampleName
+
'
/Dat_files/bg_Dat/
'
)
# Here we extract some of the data from the class to use it later,
# when we work with the sample and not the BG
# Here we extract some of the data from the background subtraction in the sample section.
bg
.
getRampPlatoLists
(
bg_heat_ranges
)
bg_plato_list
=
bg
.
plato_list
bg_ramp_list
=
bg
.
ramp_list
# Save everthing done to a log file.
bg
.
PrintLogFile
(
rootdir
+
'
/processed/
'
+
meas_sampleName
+
'
/Log_files/bg_Log/
'
)
# Finish for the BG part: Now to the real sample
#-----------------------------------------------------------------------------------------#
...
...
@@ -152,7 +151,6 @@ endScan = meas.platoend_index
# Also here we process and save to .dat
meas
.
outputDatFile
(
rootdir
+
'
/processed/
'
+
meas_sampleName
+
'
/Dat_files/meas_type1_uncorrected_Dat/
'
)
original
=
meas
.
I
# Finish loading the sample: Now to the BG subtraction and PDF generation
#-----------------------------------------------------------------------------------------#
...
...
@@ -168,10 +166,11 @@ original = meas.I
#Background subtraction, filtering and baseline correction
meas
.
getRampPlatoLists
(
meas_heat_ranges
)
meas
.
bgSubtraction
(
bg
_
plato_list
,
bg
_
ramp_list
,
meas_heat_ranges
,
bg_sampleName
,
FactorMax
=
FactorMax
,
Qmaxinst
=
Qmaxinst
,
meas
.
bgSubtraction
(
bg
.
plato_list
,
bg
.
ramp_list
,
meas_heat_ranges
,
bg_sampleName
,
FactorMax
=
FactorMax
,
Qmaxinst
=
Qmaxinst
,
empty_glas_int
=
empty_glas_int
,
empty_glas
=
empty_glas
,
Qmin
=
Qmin
,
use_PDF_maximization
=
use_PDF_maximization
,
outputPath
=
rootdir
+
'
/processed/
'
+
meas_sampleName
+
'
/PDF_files/meas_type1_uncorrected_PDF/
'
,
single_BG_file
=
r
'
C:/Users/admin/Nextcloud/MyData/bt_1222/in_situ_reactions/varex/data/Normed_and_Averaged/lk_zns_background_insitu_oaws_1_00001_002-n=None/lk_zns_background_insitu_oaws_1_00001-17040.chi
'
)
meas
.
outputMatFile
(
rootdir
+
'
/processed/
'
+
meas_sampleName
+
'
/Mat_files/meas_type1_uncorrected_Mat/
'
)
meas
.
PrintLogFile
(
rootdir
+
'
/processed/
'
+
meas_sampleName
+
'
/Log_files/meas_type1_uncorrected_Log/
'
)
...
...
@@ -190,30 +189,5 @@ meas.checkPhases(check_phases_at_scan,references=references,savefig='png',output
# In addition 2D and 1D plots of the data over time can be plottet
meas
.
plot2dTemp
(
savefig
=
'
svg
'
,
outputPath
=
rootdir
+
'
/processed/
'
+
meas_sampleName
+
'
/XRD_Plots/meas_2D_plot/
'
)
meas
.
plot1dvsTime
(
step_width
=
2
,
maxQ
=
15
,
max_index
=
30
,
plot_temp
=
True
,
savefig
=
'
svg
'
,
outputPath
=
rootdir
+
'
/processed/
'
+
meas_sampleName
+
'
/XRD_Plots/meas_1D_plot/
'
)
#~~~~~~~~~~~~~~~~~ XRD Phase Check end ~~~~~~~~~~~~~~~~~~~~~#
# Now we come to the PDf generation itself (appart from the one performed for BG subtraction)
#-----------------------------------------------------------------------------------------#
# In the beginning I tried with 3 types of aproches
# 1. Giving PDFgetX3 the sample and BG file + the subtraction factor (no corrections done)
# --> This is now implemented directly in the BG subtraction, when using PDF maximization for it.
# 2. Subtracting the BG and the give PDFgetX3 just the subtracted sample file
# (This approche works not that well as PDFgetX3 accounts for the BG subtraction scale and alters the PDF in a profidable manner,
# however here one can do baseline corrections quite easily)
# 3. Doing the corrections first, then accounting for the scale of the BG and subracting the corrections from both BG and sample,
# then giving PDFgetX3 both corrected files and the scale
# (This approche can be helpfull, but in the end corrections are after the FT not that important as a good BG subtraction)
# The difference between Qmaxinst and Qmaxinst_integrate is just that one is used as a mask for the BG subtraction
# and the other as the limit for PDFgetX3. Often they can be set just to be the same,
# so I didn´t incllude 2 varibles in the class and I now set the here:
Qmaxinst
=
Qmaxinst_integrate
#This line is used already in the phase check but is missing if one comments it out,
# because you already now the data set and just want to reprocess the PDF.
meas
.
I
=
meas
.
subtracted_I
# Here we create the .dat for PDFgetX3 to take:
meas
.
outputDatFile
(
rootdir
+
'
/processed/
'
+
meas_sampleName
+
'
/Dat_files/meas_type2_corrected_prior_Dat/
'
)
This diff is collapsed.
Click to expand it.
Preview
0%
Loading
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Save comment
Cancel
Please
register
or
sign in
to comment