{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# More detailed walkthrough" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "See the simple walkthrough for a quicker introduction to the PyDDM package. Here, we will go into a little more depth." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "
<xarray.Dataset>\n", "Dimensions: (lagtime: 40, q_y: 128, q_x: 128, q: 64, y: 128, x: 128, frames: 40)\n", "Coordinates:\n", " * lagtime (lagtime) float64 0.02398 0.04796 0.07194 ... 12.59 14.36\n", " framelag (frames) int32 1 2 3 4 5 6 7 ... 308 352 402 459 525 599\n", " * q_y (q_y) float64 -12.98 -12.78 -12.58 ... 12.37 12.58 12.78\n", " * q_x (q_x) float64 -12.98 -12.78 -12.58 ... 12.37 12.58 12.78\n", " * q (q) float64 0.0 0.2028 0.4057 0.6085 ... 12.37 12.58 12.78\n", " * y (y) int32 0 1 2 3 4 5 6 7 ... 121 122 123 124 125 126 127\n", " * x (x) int32 0 1 2 3 4 5 6 7 ... 121 122 123 124 125 126 127\n", "Dimensions without coordinates: frames\n", "Data variables:\n", " ddm_matrix_full (lagtime, q_y, q_x) float64 194.5 183.5 ... 192.0 196.8\n", " ddm_matrix (lagtime, q) float64 0.0 294.2 321.4 ... 207.8 201.1 200.4\n", " first_image (y, x) float64 128.0 149.0 173.0 ... 175.0 229.0 215.0\n", " avg_image_ft (q) float64 0.0 1.293e+05 5.225e+03 ... 105.3 104.7 105.3\n", " num_pairs_per_dt (lagtime) int32 2999 2998 2997 1498 1498 ... 20 17 15 13\n", " B float64 211.2\n", " B_std float64 1.491\n", " Amplitude (q) float64 -211.2 2.585e+05 1.024e+04 ... -1.699 -0.52\n", " ISF (lagtime, q) float64 0.0 0.9997 0.9892 ... -4.952 -19.73\n", "Attributes: (12/24)\n", " units: Intensity\n", " lagtime: sec\n", " q: μm$^{-1}$\n", " x: pixels\n", " y: pixels\n", " info: ddm_matrix is the averages of FFT difference ima...\n", " ... ...\n", " split_into_4_rois: no\n", " use_windowing_function: no\n", " binning: no\n", " bin_size: 2\n", " central_angle: no\n", " angle_range: no
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array(211.17365621)
array(1.49105881)
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<xarray.Dataset>\n", "Dimensions: (lagtime: 40, q_y: 128, q_x: 128, q: 64, y: 128, x: 128, frames: 40)\n", "Coordinates:\n", " * lagtime (lagtime) float64 0.02398 0.04796 0.07194 ... 12.59 14.36\n", " framelag (frames) int32 1 2 3 4 5 6 7 ... 308 352 402 459 525 599\n", " * q_y (q_y) float64 -12.98 -12.78 -12.58 ... 12.37 12.58 12.78\n", " * q_x (q_x) float64 -12.98 -12.78 -12.58 ... 12.37 12.58 12.78\n", " * q (q) float64 0.0 0.2028 0.4057 0.6085 ... 12.37 12.58 12.78\n", " * y (y) int32 0 1 2 3 4 5 6 7 ... 121 122 123 124 125 126 127\n", " * x (x) int32 0 1 2 3 4 5 6 7 ... 121 122 123 124 125 126 127\n", "Dimensions without coordinates: frames\n", "Data variables:\n", " ddm_matrix_full (lagtime, q_y, q_x) float64 194.5 183.5 ... 192.0 196.8\n", " ddm_matrix (lagtime, q) float64 0.0 294.2 321.4 ... 207.8 201.1 200.4\n", " first_image (y, x) float64 128.0 149.0 173.0 ... 175.0 229.0 215.0\n", " avg_image_ft (q) float64 0.0 1.293e+05 5.225e+03 ... 105.3 104.7 105.3\n", " num_pairs_per_dt (lagtime) int32 2999 2998 2997 1498 1498 ... 20 17 15 13\n", " B float64 211.2\n", " B_std float64 1.491\n", " Amplitude (q) float64 -211.2 2.585e+05 1.024e+04 ... -1.699 -0.52\n", " ISF (lagtime, q) float64 0.0 0.9997 0.9892 ... -4.952 -19.73\n", "Attributes: (12/24)\n", " units: Intensity\n", " lagtime: sec\n", " q: μm$^{-1}$\n", " x: pixels\n", " y: pixels\n", " info: ddm_matrix is the averages of FFT difference ima...\n", " ... ...\n", " split_into_4_rois: no\n", " use_windowing_function: no\n", " binning: no\n", " bin_size: 2\n", " central_angle: no\n", " angle_range: no
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array(211.17365621)
array(1.49105881)
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<xarray.Dataset>\n", "Dimensions: (lagtime: 40, q_y: 128, q_x: 128, q: 64, y: 128, x: 128, frames: 40)\n", "Coordinates:\n", " * lagtime (lagtime) float64 0.02398 0.04796 0.07194 ... 12.59 14.36\n", " framelag (frames) int32 1 2 3 4 5 6 7 ... 308 352 402 459 525 599\n", " * q_y (q_y) float64 -12.98 -12.78 -12.58 ... 12.37 12.58 12.78\n", " * q_x (q_x) float64 -12.98 -12.78 -12.58 ... 12.37 12.58 12.78\n", " * q (q) float64 0.0 0.2028 0.4057 0.6085 ... 12.37 12.58 12.78\n", " * y (y) int32 0 1 2 3 4 5 6 7 ... 121 122 123 124 125 126 127\n", " * x (x) int32 0 1 2 3 4 5 6 7 ... 121 122 123 124 125 126 127\n", "Dimensions without coordinates: frames\n", "Data variables:\n", " ddm_matrix_full (lagtime, q_y, q_x) float64 194.5 183.5 ... 192.0 196.8\n", " ddm_matrix (lagtime, q) float64 0.0 294.2 321.4 ... 207.8 201.1 200.4\n", " first_image (y, x) float64 128.0 149.0 173.0 ... 175.0 229.0 215.0\n", " avg_image_ft (q) float64 0.0 1.293e+05 5.225e+03 ... 105.3 104.7 105.3\n", " num_pairs_per_dt (lagtime) int32 2999 2998 2997 1498 1498 ... 20 17 15 13\n", " B int32 190\n", " B_std float64 1.491\n", " Amplitude (q) float64 -190.0 2.585e+05 1.026e+04 ... 19.47 20.65\n", " ISF (lagtime, q) float64 0.0 0.9996 0.9872 ... 0.432 0.4966\n", "Attributes: (12/24)\n", " units: Intensity\n", " lagtime: sec\n", " q: μm$^{-1}$\n", " x: pixels\n", " y: pixels\n", " info: ddm_matrix is the averages of FFT difference ima...\n", " ... ...\n", " split_into_4_rois: no\n", " use_windowing_function: no\n", " binning: no\n", " bin_size: 2\n", " central_angle: no\n", " angle_range: no
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array(190)
array(1.49105881)
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\n", " | Initial guess | \n", "Minimum | \n", "Maximum | \n", "
---|---|---|---|
Amplitude | \n", "100.0 | \n", "1.000 | \n", "1000000.0 | \n", "
Tau | \n", "1.0 | \n", "0.001 | \n", "10.0 | \n", "
Background | \n", "25000.0 | \n", "0.000 | \n", "10000000.0 | \n", "
StretchingExp | \n", "1.0 | \n", "0.500 | \n", "1.1 | \n", "
<xarray.Dataset>\n", "Dimensions: (parameter: 4, q: 64, lagtime: 40)\n", "Coordinates:\n", " * parameter (parameter) <U13 'Amplitude' 'Tau' ... 'StretchingExp'\n", " * q (q) float64 0.0 0.2028 0.4057 0.6085 ... 12.37 12.58 12.78\n", " * lagtime (lagtime) float64 0.02398 0.04796 0.07194 ... 12.59 14.36\n", "Data variables:\n", " parameters (parameter, q) float64 1.0 2.326e+05 ... 0.705 0.7446\n", " theory (lagtime, q) float64 10.0 315.0 338.5 ... 206.7 206.8 206.9\n", " isf_data (lagtime, q) float64 0.0 0.9996 0.9872 ... 0.432 0.4966\n", " ddm_matrix_data (lagtime, q) float64 0.0 294.2 321.4 ... 207.8 201.1 200.4\n", " A (q) float64 -190.0 2.585e+05 1.026e+04 ... 19.47 20.65\n", " B int32 190\n", "Attributes: (12/18)\n", " model: DDM Matrix - Single Exponential\n", " data_to_use: DDM Matrix\n", " initial_params_dict: ["{'n': 0, 'value': 100.0, 'limits': [1.0...\n", " effective_diffusion_coeff: 0.6168642315520588\n", " tau_vs_q_slope: [-1.98005917]\n", " msd_alpha: [1.01007082]\n", " ... ...\n", " DataDirectory: C:/Users/rmcgorty/Documents/GitHub/PyDDM/...\n", " FileName: images_nobin_40x_128x128_8bit.tif\n", " pixel_size: 0.242\n", " frame_rate: 41.7\n", " BackgroundMethod: None\n", " OverlapMethod: 2
array(['Amplitude', 'Tau', 'Background', 'StretchingExp'], dtype='<U13')
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array(190)