Merge pull request #113 from jakirkham/dn_gauss_space

Use spatial Gaussian filter in denoising

Author: jakirkham

nanshe_ipython.ipynb

@@ -448,7 +448,7 @@
         "\n",
         "\n",
         "med_filt_size = 3\n",
-        "norm_filt_sigma = 100\n",
+        "norm_filt_sigma = 10\n",
         "\n",
         "block_frames = 1\n",
         "norm_frames = 100\n",
@@ -475,19 +475,9 @@
         "            da_imgs_flt, (1,) + (da_imgs_flt.ndim - 1) * (med_filt_size,)\n",
         "        )\n",
         "\n",
-        "        # Compute the FFT of frames\n",
-        "        da_imgs_medf_fft = rfftn(da_imgs_medf, axes=tuple(irange(1, da_imgs_medf.ndim)))\n",
-        "\n",
-        "        # Smooth frames in FFT space (using a large Gaussian)\n",
-        "        da_imgs_smoothed_fft = dask_ndfourier.fourier_gaussian(\n",
-        "            da_imgs_medf_fft, (0,) + (da_imgs_medf_fft.ndim - 1) * (norm_filt_sigma,)\n",
-        "        )\n",
-        "\n",
-        "        # Inverse FFT of smoothed frames\n",
-        "        da_imgs_smoothed = irfftn(\n",
-        "            da_imgs_smoothed_fft,\n",
-        "            s=da_imgs_medf.shape[1:],\n",
-        "            axes=tuple(irange(1, da_imgs_smoothed_fft.ndim))\n",
+        "        # Compute the Gaussian filter of frames\n",
+        "        da_imgs_smoothed = dask_ndfilters.gaussian_filter(\n",
+        "            da_imgs_medf, (0,) + (da_imgs_medf.ndim - 1) * (norm_filt_sigma,)\n",
         "        )\n",
         "\n",
         "        # Apply high pass filter to images\n",