basic course content added, more TODO

courses/uoph410-510a_Image-Analysis/wk2/s2.py

@@ -0,0 +1,357 @@
+import marimo
+
+__generated_with = "0.19.11"
+app = marimo.App(width="medium")
+
+
+@app.cell
+def _():
+    import marimo as mo
+
+    return (mo,)
+
+
+@app.cell
+def _():
+    import matplotlib, matplotlib.pyplot as plt
+    plt.ion()
+    return (plt,)
+
+
+@app.cell
+def _():
+    import numpy as np
+
+    return (np,)
+
+
+@app.cell
+def _():
+    from skimage import io
+    from skimage.filters import threshold_otsu, threshold_local
+
+    return io, threshold_local, threshold_otsu
+
+
+@app.cell
+def _(mo):
+    from pathlib import Path
+    mo.pdf(src=Path("Homework2.pdf"), width="100%", height="50vh")
+    return
+
+
+@app.cell(hide_code=True)
+def _(mo):
+    mo.md(r"""
+    ## 1. Thresholding
+    """)
+    return
+
+
+@app.cell
+def _(io):
+    robert_mapplethrope_calla_lily_1984_png = io.imread("robert-mapplethrope-calla-lily-1984.png", as_gray=True)
+    return (robert_mapplethrope_calla_lily_1984_png,)
+
+
+@app.cell
+def _(plt, robert_mapplethrope_calla_lily_1984_png):
+    fig1, ax1 = plt.subplots()
+    p1 = ax1.imshow(robert_mapplethrope_calla_lily_1984_png, cmap="gray")
+    fig1.colorbar(p1, ax=ax1)
+    fig1
+    return
+
+
+@app.cell
+def _(robert_mapplethrope_calla_lily_1984_png, threshold_otsu):
+    robert_mapplethrope_calla_lily_global_threshold = threshold_otsu(robert_mapplethrope_calla_lily_1984_png)
+    robert_mapplethrope_calla_lily_global_threshold # print
+    return (robert_mapplethrope_calla_lily_global_threshold,)
+
+
+@app.cell
+def _(
+    plt,
+    robert_mapplethrope_calla_lily_1984_png,
+    robert_mapplethrope_calla_lily_global_threshold,
+):
+    fig2, (ax2a, ax2b) = plt.subplots(1, 2, figsize=(8, 4))
+    ax2a.hist(robert_mapplethrope_calla_lily_1984_png.flatten(), log=True, bins="auto")
+    ax2a.vlines(robert_mapplethrope_calla_lily_global_threshold, 0, 80_000, color="r")
+    p2b = ax2b.imshow(robert_mapplethrope_calla_lily_1984_png > robert_mapplethrope_calla_lily_global_threshold, cmap="gray")
+    fig2.colorbar(p2b, ax=ax2b)
+    fig2
+    return
+
+
+@app.cell
+def _(io, plt):
+    fig3, ax3 = plt.subplots()
+    istanbul_arch_museum_gray_crop_png = io.imread("istanbul_arch_museum_gray_crop.png", as_gray=True)
+    p3 = ax3.imshow(istanbul_arch_museum_gray_crop_png, cmap="gray")
+    fig3.colorbar(p3, ax=ax3)
+    fig3
+    return (istanbul_arch_museum_gray_crop_png,)
+
+
+@app.cell
+def _(istanbul_arch_museum_gray_crop_png, threshold_otsu):
+    istanbul_global_threshold = threshold_otsu(istanbul_arch_museum_gray_crop_png)
+    istanbul_global_threshold # print
+    return (istanbul_global_threshold,)
+
+
+@app.cell
+def _(istanbul_arch_museum_gray_crop_png, istanbul_global_threshold, plt):
+    fig4, (ax4a, ax4b) = plt.subplots(1, 2, figsize=(8, 4))
+    ax4a.hist(istanbul_arch_museum_gray_crop_png.flatten(), log=True, bins="auto")
+    ax4a.vlines(istanbul_global_threshold, 0, 300_000, color='r')
+    p4b = ax4b.imshow(istanbul_arch_museum_gray_crop_png > istanbul_global_threshold, cmap="gray")
+    fig4.colorbar(p4b, ax=ax4b)
+    fig4
+    return
+
+
+@app.cell
+def _(io):
+    robert_mapplethrope_calla_lily_1984_crop_png = io.imread("robert-mapplethrope-calla-lily-1984_CROP.png", as_gray=True)
+    return (robert_mapplethrope_calla_lily_1984_crop_png,)
+
+
+@app.cell
+def _(plt, robert_mapplethrope_calla_lily_1984_crop_png):
+    fig5, ax5 = plt.subplots()
+    p5 = ax5.imshow(robert_mapplethrope_calla_lily_1984_crop_png, cmap="gray")
+    fig5.colorbar(p5, ax=ax5)
+    fig5
+    return
+
+
+@app.cell
+def _(robert_mapplethrope_calla_lily_1984_crop_png, threshold_otsu):
+    robert_mapplethrope_calla_lily_crop_global_threshold = threshold_otsu(robert_mapplethrope_calla_lily_1984_crop_png)
+    robert_mapplethrope_calla_lily_crop_global_threshold # print
+    return (robert_mapplethrope_calla_lily_crop_global_threshold,)
+
+
+@app.cell
+def _(
+    plt,
+    robert_mapplethrope_calla_lily_1984_crop_png,
+    robert_mapplethrope_calla_lily_crop_global_threshold,
+):
+    fig6, (ax6a, ax6b) = plt.subplots(1, 2, figsize=(8, 4))
+    ax6a.hist(robert_mapplethrope_calla_lily_1984_crop_png.flatten(), log=True, bins="auto")
+    ax6a.vlines(robert_mapplethrope_calla_lily_crop_global_threshold, 0, 80_000, color="r")
+    p6b = ax6b.imshow(robert_mapplethrope_calla_lily_1984_crop_png > robert_mapplethrope_calla_lily_crop_global_threshold, cmap="gray")
+    fig6.colorbar(p6b, ax=ax6b)
+    fig6
+    return
+
+
+@app.cell(hide_code=True)
+def _(mo):
+    mo.md(r"""
+    ## 2. Thresholding, again
+    """)
+    return
+
+
+@app.cell
+def _(
+    istanbul_arch_museum_gray_crop_png,
+    plt,
+    robert_mapplethrope_calla_lily_1984_crop_png,
+    robert_mapplethrope_calla_lily_1984_png,
+    threshold_local,
+):
+    fig7, (ax7a, ax7b, ax7c) = plt.subplots(1, 3, figsize=(12, 4))
+    p7a = ax7a.imshow(robert_mapplethrope_calla_lily_1984_png > threshold_local(robert_mapplethrope_calla_lily_1984_png, block_size=123), cmap="gray")
+    fig7.colorbar(p7a, ax=ax7a)
+    p7b = ax7b.imshow(istanbul_arch_museum_gray_crop_png > threshold_local(istanbul_arch_museum_gray_crop_png, block_size=123), cmap="gray")
+    fig7.colorbar(p7b, ax=ax7b)
+    p7c = ax7c.imshow(robert_mapplethrope_calla_lily_1984_crop_png > threshold_local(robert_mapplethrope_calla_lily_1984_crop_png, block_size=123), cmap="gray")
+    fig7.colorbar(p7c, ax=ax7c)
+    fig7
+    return
+
+
+@app.cell(hide_code=True)
+def _(mo):
+    mo.md(r"""
+    ## 3. Protein density
+    """)
+    return
+
+
+@app.cell
+def _(io, plt):
+    fig8, ax8 = plt.subplots()
+    microarray_crop_png = io.imread("microarray_crop.png", as_gray=True)
+    p8 = ax8.imshow(microarray_crop_png, cmap="gray")
+    fig8.colorbar(p8, ax=ax8)
+    fig8
+    return
+
+
+@app.cell(hide_code=True)
+def _(mo):
+    mo.md(r"""
+    ## 4. Non-uniform background subtraction
+    """)
+    return
+
+
+@app.cell
+def _(io, plt):
+    fig9, ax9 = plt.subplots()
+    GUV24_bead_crop_png = io.imread("GUV24_bead_Crop.png", as_gray=True)
+    p9 = ax9.imshow(GUV24_bead_crop_png, cmap="gray")
+    fig9.colorbar(p9, ax=ax9)
+    fig9
+    return (GUV24_bead_crop_png,)
+
+
+@app.cell
+def _(GUV24_bead_crop_png, np):
+    x = np.arange(GUV24_bead_crop_png.shape[0])
+    y = np.arange(GUV24_bead_crop_png.shape[1])
+    xs, ys = np.meshgrid(x, y)
+    return x, xs, ys
+
+
+@app.cell
+def _(GUV24_bead_crop_png, plt, xs, ys):
+    fig10, ax10 = plt.subplots()
+    ax10 = plt.axes(projection ='3d')
+    p10 = ax10.plot_surface(xs, ys, GUV24_bead_crop_png, cmap="viridis")
+    fig10
+    return
+
+
+@app.cell(hide_code=True)
+def _(mo):
+    mo.md(r"""
+    ### b.
+    """)
+    return
+
+
+@app.cell
+def _(GUV24_bead_crop_png, np, xs):
+    w = np.vstack([xs.ravel(), np.ones(xs.size)]).T
+    mx, c = np.linalg.lstsq(w, GUV24_bead_crop_png.ravel())[0] # (c-410) 3pt alternative
+    (mx, c)
+    return c, mx
+
+
+@app.cell
+def _(GUV24_bead_crop_png, c, mx, plt, x, xs, ys):
+    fig11, (ax11a, ax11b) = plt.subplots(1, 2, figsize=(8, 4))
+    ax11a.plot(x, mx * x + c, c='r')
+    ax11a.scatter(xs.ravel(), GUV24_bead_crop_png.ravel(), s=4)
+    ax11b.scatter(ys.ravel(), GUV24_bead_crop_png.ravel(), s=4)
+    fig11
+    return
+
+
+@app.cell(hide_code=True)
+def _(mo):
+    mo.md(r"""
+    ### c.
+    #### 410:
+    """)
+    return
+
+
+@app.cell
+def _(GUV24_bead_crop_png, np, xs, ys):
+    # z = m @ w + c
+    w2 = np.vstack([xs.ravel(), ys.ravel(), np.ones(GUV24_bead_crop_png.size)]).T
+    mx2, my2, c2 = np.linalg.lstsq(w2, GUV24_bead_crop_png.ravel())[0]
+    (mx2, my2, c2)
+    return c2, mx2, my2
+
+
+@app.cell
+def _(GUV24_bead_crop_png, c2, mx2, my2, plt, xs, ys):
+    fig12, ax12 = plt.subplots()
+    ax12 = plt.axes(projection ='3d')
+    ax12.plot_surface(xs, ys, GUV24_bead_crop_png, cmap="viridis", alpha=0.3)
+    ax12.plot_surface(xs, ys, mx2 * xs + my2 * ys + c2, cmap="plasma")
+    fig12
+    return
+
+
+@app.cell
+def _(GUV24_bead_crop_png, c2, mx2, my2, plt, xs, ys):
+    fig13, ax13 = plt.subplots()
+    ax13 = plt.axes(projection ='3d')
+    ax13.plot_surface(xs, ys, GUV24_bead_crop_png - (mx2 * xs + my2 * ys + c2), cmap="viridis")
+    fig13
+    return
+
+
+@app.cell
+def _(GUV24_bead_crop_png, c2, mx2, my2, plt, xs, ys):
+    fig14, ax14 = plt.subplots()
+    p14 = ax14.imshow(GUV24_bead_crop_png - (mx2 * xs + my2 * ys + c2), cmap="gray")
+    fig14.colorbar(p14, ax=ax14)
+    fig14
+    return
+
+
+@app.cell(hide_code=True)
+def _(mo):
+    mo.md(r"""
+    #### 510:
+    """)
+    return
+
+
+@app.cell
+def _(GUV24_bead_crop_png, np, xs, ys):
+    # z = m @ w + c
+    w3 = np.vstack([xs.ravel(), np.square(xs.ravel()), 
+                   ys.ravel(), np.square(ys.ravel()), 
+                   np.ones(GUV24_bead_crop_png.size)]).T
+    mx3, mx3x, my3, my3y, c3 = np.linalg.lstsq(w3, GUV24_bead_crop_png.ravel())[0]
+    (mx3, mx3x, my3, my3y, c3)
+    return c3, mx3, mx3x, my3, my3y
+
+
+@app.cell
+def _(GUV24_bead_crop_png, c3, mx3, mx3x, my3, my3y, np, plt, xs, ys):
+    fig15, ax15 = plt.subplots()
+    ax15 = plt.axes(projection ='3d')
+    ax15.plot_surface(xs, ys, GUV24_bead_crop_png, cmap="viridis", alpha=0.3)
+    ax15.plot_surface(xs, ys, mx3 * xs + mx3x * np.square(xs) + my3 * ys + my3y * np.square(ys) + c3, cmap="plasma")
+    return
+
+
+@app.cell
+def _(GUV24_bead_crop_png, c3, mx3, mx3x, my3, my3y, np, plt, xs, ys):
+    fig16, ax16 = plt.subplots()
+    p16 = ax16.imshow(GUV24_bead_crop_png - (mx3 * xs + mx3x * np.square(xs) + my3 * ys + my3y * np.square(ys) + c3), cmap="gray")
+    fig16.colorbar(p16, ax=ax16)
+    fig16
+    return
+
+
+@app.cell
+def _(GUV24_bead_crop_png, c3, mx3, mx3x, my3, my3y, np, plt, xs, ys):
+    fig17, ax17 = plt.subplots()
+    ax17 = plt.axes(projection ='3d')
+    ax17.plot_surface(xs, ys, GUV24_bead_crop_png - 
+                    (mx3 * xs + mx3x * np.square(xs) + my3 * ys + my3y * np.square(ys) + c3), cmap="viridis")
+    return
+
+
+@app.cell
+def _():
+    return
+
+
+if __name__ == "__main__":
+    app.run()