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WIP: Add difference step #107

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WIP: Add difference step #107

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62 changes: 61 additions & 1 deletion nanshe_ipython.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -51,6 +51,7 @@
"postfix_sub = \"_sub\"\n",
"postfix_f_f0 = \"_f_f0\"\n",
"postfix_wt = \"_wt\"\n",
"postfix_diff = \"_diff\"\n",
"postfix_norm = \"_norm\"\n",
"postfix_dict = \"_dict\"\n",
"postfix_post = \"_post\"\n",
Expand Down Expand Up @@ -989,6 +990,65 @@
" )"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Difference\n",
"\n",
"* `block_space` (`int`): extent of each spatial dimension for each block (run in parallel).\n",
"* `norm_frames` (`int`): number of frames for use during normalization of each full frame block (run in parallel)."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"%%time\n",
"\n",
"\n",
"block_frames = 40\n",
"norm_frames = 100\n",
"\n",
"\n",
"with get_executor(client) as executor:\n",
" dask_io_remove(data_basename + postfix_diff + zarr_ext, executor)\n",
"\n",
"\n",
" with open_zarr(data_basename + postfix_wt + zarr_ext, \"r\") as f:\n",
" # Load and prep data for computation.\n",
" imgs = f[\"images\"]\n",
" da_imgs = da.from_array(\n",
" imgs, chunks=(block_frames,) + (imgs.ndim - 1) * (block_space,)\n",
" )\n",
"\n",
" da_imgs_flt = da_imgs\n",
" if not (issubclass(da_imgs_flt.dtype.type, np.floating) and \n",
" da_imgs_flt.dtype.itemsize >= 4):\n",
" da_imgs_flt = da_imgs_flt.astype(np.float32)\n",
"\n",
" da_result = da_imgs_flt[1:] - da_imgs_flt[:-1]\n",
"\n",
" # Store denoised data\n",
" dask_store_zarr(data_basename + postfix_diff + zarr_ext, [\"images\"], [da_result], executor)\n",
"\n",
"\n",
" zip_zarr(data_basename + postfix_diff + zarr_ext, executor)\n",
"\n",
"\n",
"if __IPYTHON__:\n",
" result_image_stack = LazyZarrDataset(data_basename + postfix_diff + zarr_ext, \"images\")\n",
"\n",
" mplsv = plt.figure(FigureClass=MPLViewer)\n",
" mplsv.set_images(\n",
" result_image_stack,\n",
" vmin=par_compute_min_projection(num_frames=norm_frames)(result_image_stack).min(),\n",
" vmax=par_compute_max_projection(num_frames=norm_frames)(result_image_stack).max()\n",
" )"
]
},
{
"cell_type": "markdown",
"metadata": {},
Expand All @@ -1015,7 +1075,7 @@
" dask_io_remove(data_basename + postfix_norm + zarr_ext, executor)\n",
"\n",
"\n",
" with open_zarr(data_basename + postfix_wt + zarr_ext, \"r\") as f:\n",
" with open_zarr(data_basename + postfix_diff + zarr_ext, \"r\") as f:\n",
" # Load and prep data for computation.\n",
" imgs = f[\"images\"]\n",
" da_imgs = da.from_array(\n",
Expand Down