napari-dpr 0.1.0__cp311-cp311-win_amd64.whl

napari_dpr/__init__.py

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+"""
+napari-dpr plugin package.
+"""
+
+__version__ = "0.1.0"
+
+# Import modules for easier access
+from napari_dpr.dpr_core import *
+from napari_dpr.dpr import * 

napari_dpr/_widget.py

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+"""
+Napari plugin widget for DPR resolution enhancement.
+"""
+from typing import TYPE_CHECKING
+import numpy as np
+from magicgui import magic_factory
+from napari_dpr.dpr_core import apply_dpr
+
+if TYPE_CHECKING:
+    import napari
+
+@magic_factory(
+    psf={"widget_type": "FloatSpinBox", "min": 1.0, "max": 10.0, "step": 0.1, "value": 4.0},
+    gain={"widget_type": "FloatSpinBox", "min": 0.1, "max": 10.0, "step": 0.1, "value": 2.0},
+    background={"widget_type": "FloatSpinBox", "min": 0.0, "max": 50.0, "step": 1.0, "value": 10.0},
+    call_button="Enhance Resolution"
+)
+def enhance_image(
+    viewer: "napari.viewer.Viewer",
+    image_layer: "napari.layers.Image",
+    psf: float = 4.0,
+    gain: float = 2.0,
+    background: float = 10.0,
+) -> None:
+    """
+    Enhance image resolution using DPR.
+    
+    Parameters
+    ----------
+    viewer : napari.viewer.Viewer
+        Napari viewer instance
+    image_layer : napari.layers.Image
+        Input image layer to enhance
+    psf : float
+        Point spread function size parameter
+    gain : float
+        Gain parameter for enhancement
+    background : float
+        Background subtraction value
+    """
+    if image_layer is None:
+        raise ValueError("Please select an image layer")
+    
+    # Get the image data
+    image_data = image_layer.data
+    
+    # Make sure image has the right dimensions and type
+    # DPR expects a 3D array (HEIGHT, WIDTH, TIME/CHANNELS)
+    if image_data.ndim == 2:
+        # Convert 2D image to 3D with one time point
+        image_data = image_data[:, :, np.newaxis]
+    elif image_data.ndim == 3 and image_data.shape[0] < image_data.shape[1]:
+        # If first dimension is smallest, it's probably [TIME, HEIGHT, WIDTH]
+        # We need to transpose to [HEIGHT, WIDTH, TIME]
+        image_data = image_data.transpose([1, 2, 0])
+    elif image_data.ndim > 3:
+        # If 4D or more, take the first 3 dimensions
+        image_data = image_data[:, :, :, 0]
+        
+    # Ensure data is float64
+    if image_data.dtype != np.float64:
+        image_data = image_data.astype(np.float64)
+    
+    # Apply DPR
+    try:
+        dpr_out, magnified = apply_dpr(image_data, psf=psf, gain=gain, background=background)
+        
+
+        
+        # Add the magnified original for comparison
+        viewer.add_image(
+            magnified.sum(axis=2),  # Sum over the time/channel dimension
+            name=f"{image_layer.name}_magnified",
+            colormap=image_layer.colormap.name,
+        )
+
+        # Add the enhanced image to the viewer
+        viewer.add_image(
+            dpr_out,
+            name=f"{image_layer.name}_DPR_enhanced",
+            colormap=image_layer.colormap.name,
+        )
+        
+    except Exception as e:
+        import traceback
+        print(f"Error applying DPR: {e}")
+        print(traceback.format_exc())
+        raise 

napari_dpr/dpr.py

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+import os, sys, time, numpy as np, scipy.ndimage as ndi
+from scipy.interpolate import RectBivariateSpline
+import tifffile as tiff
+from PIL import Image
+import matplotlib.pyplot as plt
+
+## original DPR as shown by https://github.com/biomicroscopy/DPR-Resolution_enhancement_with_deblurring_by_pixel_reassignment
+
+def dpr_set_parameters(psf, **k): return {'gain': k.get('gain',1), 'background': k.get('background',int(np.ceil(17*psf))), 'temporal': k.get('temporal',None)}
+
+def dpr_update_single(i, psf, opt):
+    g, r = opt['gain'], int(np.ceil(opt['background']))
+    psf /= 1.6651
+    h, w = i.shape
+    x0, y0 = np.linspace(-.5,.5,w), np.linspace(-.5,.5,h)
+    x, y = np.linspace(-.5,.5,round(5*w/psf)), np.linspace(-.5,.5,round(5*h/psf))
+    sx, sy = np.array([[1,0,-1],[2,0,-2],[1,0,-1]]), np.array([[1,2,1],[0,0,0],[-1,-2,-1]])
+    i = i - i.min()
+    localmin = np.zeros_like(i)
+    i_localmin = np.zeros_like(i)
+    for u in range(h):
+        for v in range(w):
+            sub = i[max(0,u-r):min(h,u+r+1), max(0,v-r):min(w,v+r+1)]
+            localmin[u,v] = sub.min()
+            i_localmin[u,v] = i[u,v] - localmin[u,v]
+    m = RectBivariateSpline(y0,x0,i_localmin)(y,x)
+    m[m<0] = 0
+    m = np.pad(m,10)
+    mag = RectBivariateSpline(y0,x0,i)(y,x)
+    mag[mag<0] = 0
+    mag = np.pad(mag,10)
+    hn, wn = mag.shape
+    norm = m / (ndi.gaussian_filter(m,10)+1e-5)
+    gx = ndi.convolve(norm, sy, mode='reflect') / (norm + 1e-5)
+    gy = ndi.convolve(norm, sx, mode='reflect') / (norm + 1e-5)
+    d = 0.5*g+1
+    dx, dy = d*gx, d*gy
+    dx[np.abs(dx)>10] = 0
+    dy[np.abs(dy)>10] = 0
+    out = np.zeros((hn, wn))
+    for nx in range(10, hn-10):
+        for ny in range(10, wn-10):
+            wx, wy = dx[nx,ny], dy[nx,ny]
+            fx, fy = int(wx), int(wy)
+            sx, sy = int(np.sign(wx)), int(np.sign(wy))
+            w1 = (1-abs(wx-fx))*(1-abs(wy-fy))
+            w2 = (1-abs(wx-fx))*abs(wy-fy)
+            w3 = abs(wx-fx)*(1-abs(wy-fy))
+            w4 = abs(wx-fx)*abs(wy-fy)
+            c1 = [fx, fy]
+            c2 = [fx, fy+sy]
+            c3 = [fx+sx, fy]
+            c4 = [fx+sx, fy+sy]
+            val = mag[nx,ny]
+            out[nx+c1[0], ny+c1[1]] += w1*val
+            out[nx+c2[0], ny+c2[1]] += w2*val
+            out[nx+c3[0], ny+c3[1]] += w3*val
+            out[nx+c4[0], ny+c4[1]] += w4*val
+    return out[10:-10,10:-10], mag[10:-10,10:-10], g, r
+
+def dpr_stack(s, psf, o):
+    f = s.shape[2]
+    shp = dpr_update_single(s[:,:,0],psf,o)[1].shape
+    out = np.zeros((*shp,f)); mag = np.zeros((*shp,f))
+    for i in range(f):
+        sys.stdout.write(f"\rProcessing {i+1}/{f}"); sys.stdout.flush()
+        o1,o2,_,_ = dpr_update_single(s[:,:,i],psf,o)
+        out[:,:,i], mag[:,:,i] = o1, o2
+    t = o.get('temporal','')
+    if t == 'mean': out = np.mean(out,axis=2)
+    elif t == 'var': out = np.var(out,axis=2)
+    return out, mag
+
+def load_image_stack(p,n,t):
+    path = os.path.join(p,f'{n}.{t}')
+    if t.lower() == 'tif':
+        d = tiff.imread(path)
+        return np.transpose(d,(1,2,0)) if d.ndim==3 else d
+    return np.array(Image.open(path))
+
+def save_image(im, p, n, t):
+    os.makedirs(p, exist_ok=True)
+    f = os.path.join(p, f'{n}.{t}')
+    if t.lower()=='tif': tiff.imwrite(f, im)
+    else:
+        if im.dtype != np.uint8:
+            im = ((im-im.min())/(im.max()-im.min())*255).astype(np.uint8)
+        Image.fromarray(im).save(f)
+
+def process_image(p,n,t,psf,o):
+    s = load_image_stack(p,n,t)
+    out, mag = dpr_stack(s, psf, o)
+    save_image(out, os.path.join(p,'DPR_results'), f'{n}_result', t)
+    return s, out, mag
+
+def display_images(i,m,o):
+    plt.figure(figsize=(12,4))
+    plt.subplot(1,3,1); plt.imshow(i[...,0] if i.ndim==3 else i, cmap='gray'); plt.title('Initial')
+    plt.subplot(1,3,2); plt.imshow(np.mean(m,axis=2) if m.ndim==3 else m, cmap='gray'); plt.title('Magnified')
+    plt.subplot(1,3,3); plt.imshow(o, cmap='gray'); plt.title('DPR')
+    plt.tight_layout(); plt.show()
+
+def main():
+    p = r'test_data'
+    f = input("File name [test_image.tif]: ") or "test_image.tif"
+    n,t = f.rsplit('.',1)
+    mode = input("Use default params? y/n/e [y]: ").lower() or 'y'
+    if mode == 'e':
+        print("PSF: blur radius\nGain: enhancement\nBackground: subtraction\nTemporal: mean or var")
+        mode = input("Use default now? y/n [y]: ").lower() or 'y'
+    if mode == 'y': psf,g,bg,tmp = 4,2,10,'mean'
+    else:
+        psf = float(input("PSF [4]: ") or 4)
+        g = float(input("Gain [2]: ") or 2)
+        bg = float(input("Background [10]: ") or 10)
+        tmp = input("Temporal [mean]: ") or 'mean'
+    o = dpr_set_parameters(psf, gain=g, background=bg, temporal=tmp)
+    start = time.time()
+    res = process_image(p,n,t,psf,o)
+    if res:
+        img,dpr,mag = res
+        print(f"\nTime: {time.time()-start:.2f}s")
+        display_images(img,mag,dpr)
+    else: print("Failed.")
+
+def apply_dpr(im, psf=4, gain=2, background=10, temporal='mean'):
+    if im.ndim == 2: im = im[:,:,np.newaxis]
+    o = dpr_set_parameters(psf, gain=gain, background=background, temporal=temporal)
+    return dpr_stack(im, psf, o)
+
+if __name__ == '__main__': main()