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fix: experiment notebook (#155)
2 parents 9746551 + 976fbe1 commit 4f92ca4

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Lines changed: 149 additions & 18 deletions

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‎notebooks/experiment.ipynb‎

Lines changed: 149 additions & 18 deletions
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@@ -1,5 +1,13 @@
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{
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"cells": [
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{
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"cell_type": "markdown",
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"id": "4f3e3089",
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"metadata": {},
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"source": [
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"Load in modules"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
@@ -19,6 +27,33 @@
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"%matplotlib inline"
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]
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},
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{
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"cell_type": "markdown",
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"id": "1bc3fec6",
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"metadata": {},
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"source": [
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"Change a default setting within defdap"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "a3d943f6",
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"metadata": {},
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"outputs": [],
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"source": [
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"from defdap import defaults\n",
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"defaults['hrdic_grain_finding_method'] = 'warp'"
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]
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},
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{
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"cell_type": "markdown",
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"id": "b99a3fe7",
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"metadata": {},
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"source": [
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"Define an empty experiment to load data into"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
@@ -29,14 +64,33 @@
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"exp = experiment.Experiment()"
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]
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},
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{
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"cell_type": "markdown",
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"id": "f619dcd6",
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"metadata": {},
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"source": [
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"Define paths to data. HRDIC path now has a wildcard '*' to use all matched files."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "2ae42113-e960-4c0c-b800-62604bfefc9f",
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"metadata": {},
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"outputs": [],
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"source": [
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"data_dir = Path('/Users/user/Downloads/small_DIC_data_set/')"
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"data_dir = Path('./')\n",
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"hrdic_dir = data_dir / 'DIC_DaVis_Export'\n",
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"hrdic_file_pattern = 'B*.txt'\n",
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"ebsd_file = data_dir / 'EBSD/Sample 2.cpr'"
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]
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},
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{
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"cell_type": "markdown",
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"id": "579fa880",
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"metadata": {},
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"source": [
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"Load HRDIC maps and place them in a new increment (default) in the experiment, but define a single frame they share to make registration easier."
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]
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},
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{
@@ -47,10 +101,18 @@
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"outputs": [],
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"source": [
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"dic_frame = experiment.Frame()\n",
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"for dic_file in sorted(data_dir.glob('B*.txt')):\n",
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"for dic_file in sorted(hrdic_dir.glob(hrdic_file_pattern)):\n",
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" hrdic.Map(dic_file, experiment=exp, frame=dic_frame)"
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]
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},
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{
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"cell_type": "markdown",
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"id": "7a37a8c4",
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"metadata": {},
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"source": [
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"Load the EBSD and place it in the first incremnet but in a different frame."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
@@ -60,11 +122,19 @@
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"source": [
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"ebsd_frame = experiment.Frame()\n",
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"ebsd.Map(\n",
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" data_dir / 'A3_zone1.cpr',\n",
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" ebsd_file,\n",
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" increment=exp.increments[0], frame=experiment.Frame()\n",
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")"
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]
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},
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{
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"cell_type": "markdown",
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"id": "34382ce4",
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"metadata": {},
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"source": [
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"Define homologous points. This only needs to be done for once for all of the HRDIC maps as they share a reference frame."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
@@ -74,58 +144,119 @@
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"source": [
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"dic_map = exp.increments[0].maps['hrdic']\n",
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"dic_map.frame.homog_points = [\n",
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" (259, 225), \n",
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" (322, 376), \n",
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" (91, 21), \n",
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" (365, 97)\n",
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" ( 806, 239), (1198, 147), (1445, 376), (1769, 790), (1622, 1341),\n",
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" (1782, 1814), (1215, 1473), ( 563, 1617), ( 728, 1295), ( 758, 1102),\n",
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" ( 483, 1161), ( 231, 1032), ( 212, 659), (1169, 1066)\n",
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"]\n",
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"\n",
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"ebsd_map = exp.increments[0].maps['ebsd']\n",
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"ebsd_map.frame.homog_points = [\n",
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" (90, 84), \n",
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" (110, 141), \n",
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" (31, 10), \n",
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" (128, 40)\n",
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" (238, 120), (324, 102), (375, 147), (440, 230), (400, 344), \n",
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" (429, 440), (310, 371), (166, 399), (207, 334), (216, 295), \n",
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" (155, 308), (102, 282), (104, 206), (306, 288)\n",
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"]"
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]
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},
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{
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"cell_type": "markdown",
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"id": "b5284775",
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"metadata": {},
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"source": [
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"Loop over all the HRIDC maps stored in the experiment to set some parameters."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "2fd94bd2-5485-485a-812a-33628c575a29",
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"id": "d663f030",
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"metadata": {},
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"outputs": [],
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"source": [
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"field_width = 30 # microns\n",
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"num_pixels = 2048\n",
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"pixel_size = field_width / num_pixels\n",
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"\n",
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"for inc, dic_map in exp.iter_over_maps('hrdic'):\n",
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" dic_map.set_crop(left=100, right=100, bottom=100, top=100)\n",
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" dic_map.link_ebsd_map(ebsd_map, transform_type=\"affine\")\n",
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" dic_map.plot_map(\n",
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" dic_map.set_scale(pixel_size)"
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]
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},
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{
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"cell_type": "markdown",
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"id": "74a998de",
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"metadata": {},
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"source": [
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"Loop over the maps and plot a subregion of each map."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "2fd94bd2-5485-485a-812a-33628c575a29",
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"metadata": {},
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"outputs": [],
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"source": [
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"for inc, dic_map in exp.iter_over_maps('hrdic'):\n",
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" plot = dic_map.plot_map(\n",
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" 'max_shear', vmin=0, vmax=0.10, \n",
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" plot_scale_bar=False, plot_gbs='line'\n",
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" )\n",
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" plot.ax.set_xlim([800, 1200])\n",
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" plot.ax.set_ylim([800, 1200])\n",
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" plt.tight_layout()"
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]
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},
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{
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"cell_type": "markdown",
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"id": "677435e4",
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"metadata": {},
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"source": [
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"As the grain segmentation is done using the same EBSD data, the grain ids for all of the HRDIC should be consistent. So pick the same grain from each time step and plot deformation data over each step."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "7fef2016-c924-41a4-8036-8240f46cc1fc",
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"metadata": {},
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"outputs": [],
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"source": []
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"source": [
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"dic_grain_id = 400\n",
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"\n",
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"num_incs = len(exp.increments)\n",
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"fig, axes = plt.subplots(2, int(np.ceil(num_incs / 2)))\n",
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"\n",
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"for inc, dic_map in exp.iter_over_maps('hrdic'):\n",
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" dic_grain = dic_map[dic_grain_id]\n",
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" plot = dic_grain.plot_map(\n",
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" 'max_shear', vmin=0, vmax=0.10, \n",
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" plot_scale_bar=(inc == 0), plot_colour_bar=False,\n",
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" fig=fig, ax=axes.flat[inc]\n",
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" )\n",
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"\n",
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"for ax in axes.flat:\n",
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" ax.axis('off')\n",
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"\n",
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"fig.subplots_adjust(right=0.8)\n",
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"cbar_ax = fig.add_axes([0.85, 0.15, 0.03, 0.7])\n",
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"fig.colorbar(plot.img_layers[0], cax=cbar_ax, label=\"Effective shear strain\")\n"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "457eba02-2eda-4fe3-b70a-40f73aae3bf1",
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"id": "f4392ca6",
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python [conda env:defdap]",
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"display_name": "workshop_test",
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"language": "python",
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"name": "conda-env-defdap-py"
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.11.0"
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"version": "3.13.13"
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}
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},
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"nbformat": 4,

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