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hackathon work on PyDDM code (frame previews, SIA curves, fits and plots) #1

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6c0efdc
hackathon work
gregorleech Aug 3, 2022
09cda8e
Update (DMREF edits) DDM - Walkthrough - More in-depth .ipynb
gregorleech Aug 3, 2022
15c5617
pre-hackathon work
gregorleech Aug 3, 2022
410b219
Merge branch 'main' of https://github.com/gregorleech/PyDDM
gregorleech Aug 3, 2022
4488c86
updates
gregorleech Aug 5, 2022
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5,399 changes: 5,399 additions & 0 deletions Examples/(DMREF edits) DDM - Walkthrough - More in-depth .ipynb
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26 changes: 26 additions & 0 deletions Examples/Achiriloaie_activeAMT_1000fr_5.yml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,26 @@
DataDirectory: '/Users/gregor/Downloads/Daisy/' #'C:/Users/Ryan/Documents/GitHub/PyDDM/Examples/'
FileName: 'Achiriloaie_activeAMT_1000fr_5.tif'
Metadata:
pixel_size: 0.81 #size of pixel in um
frame_rate: 2.65 #frames per second
Analysis_parameters:
starting_frame_number: 0
ending_frame_number: 999
number_lagtimes: 40
first_lag_time: 1
last_lag_time: 600
crop_to_roi: null # set to 'null' (no quotes) for no cropping [topleft,bottomleft,topright,bottomright]
split_into_4_rois: no
use_windowing_function: no #Use Blackmann-Harris windowing or not?
binning: yes
bin_size: 2
central_angle: null
angle_range: null
Fitting_parameters:
model: 'DDM Matrix - Single Exponential' #Options are 'ISF - Single Exponential' and ...
Tau: [1.0, 0.001, 10]
StretchingExp: [1.0, 0.5, 1.1]
Amplitude: [1e2, 1, 1e6]
Background: [2.5e4, 0, 1e7]
Good_q_range: [5, 20]
Auto_update_good_q_range: True
26 changes: 26 additions & 0 deletions Examples/Achiriloaie_activeAMT_1000fr_7.yml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,26 @@
DataDirectory: '/Users/gregor/Downloads/Daisy/' #'C:/Users/Ryan/Documents/GitHub/PyDDM/Examples/'
FileName: 'Achiriloaie_activeAMT_1000fr_7.tif'
Metadata:
pixel_size: 0.81 #size of pixel in um
frame_rate: 2.65 #frames per second
Analysis_parameters:
starting_frame_number: 0
ending_frame_number: 999
number_lagtimes: 40
first_lag_time: 1
last_lag_time: 600
crop_to_roi: null # set to 'null' (no quotes) for no cropping [topleft,bottomleft,topright,bottomright]
split_into_4_rois: no
use_windowing_function: no #Use Blackmann-Harris windowing or not?
binning: yes
bin_size: 2
central_angle: null
angle_range: null
Fitting_parameters:
model: 'DDM Matrix - Single Exponential' #Options are 'ISF - Single Exponential' and ...
Tau: [1.0, 0.001, 10]
StretchingExp: [1.0, 0.5, 1.1]
Amplitude: [1e2, 1, 1e6]
Background: [2.5e4, 0, 1e7]
Good_q_range: [5, 20]
Auto_update_good_q_range: True
8 changes: 5 additions & 3 deletions Examples/DDM - Walkthrough - Diffusing Silica Beads - More in-depth.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -120,7 +120,9 @@
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"metadata": {
"scrolled": false
},
"outputs": [
{
"name": "stdout",
Expand Down Expand Up @@ -4817,7 +4819,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -4831,7 +4833,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.4"
"version": "3.9.12"
},
"toc-autonumbering": false,
"toc-showcode": false,
Expand Down
8 changes: 5 additions & 3 deletions Examples/DDM - Walkthrough - Diffusing Silica Beads - Simple.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -3944,7 +3944,9 @@
"metadata": {},
"outputs": [],
"source": [
"ddm.save_fit_results_to_excel(fit01)"
"ddm.save_fit_results_to_excel(fit01)\n",
"fit01.to_netcdf(\"example_netcdf_file.nc\")\n",
"loaded_netcdf_file = xr.open_dataset(\"example_netcdf_file.nc\")"
]
},
{
Expand Down Expand Up @@ -3975,7 +3977,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -3989,7 +3991,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.5"
"version": "3.9.12"
},
"toc-autonumbering": false,
"toc-showcode": false,
Expand Down
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