diff --git a/zarr.ipynb b/zarr.ipynb
index 4397ca56086c6c4a44e2ae62fe2e32faaf3cffee..91057eddcd99e9d6a0517ea8f75c59873d01a641 100644
--- a/zarr.ipynb
+++ b/zarr.ipynb
@@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
- "execution_count": 17,
+ "execution_count": 1,
"id": "13ddd473-b4d6-4af2-94d3-c1cfd82022d0",
"metadata": {},
"outputs": [],
@@ -18,7 +18,7 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 3,
"id": "2a06e28a-d15d-4804-a343-f49e42b47594",
"metadata": {},
"outputs": [],
@@ -27,17 +27,40 @@
" img = aicsimageio.imread_dask(path)\n",
" print(img)\n",
" if chunksize is not None:\n",
- " img = img.rechunk((1,1,156,128,128))\n",
+ " img = img.rechunk(chunksize)\n",
+ " print(\"rechunk\",img)\n",
" baseurl = path.replace(path.split('.')[-1], \"zarr\")\n",
+ " print(baseurl)\n",
+ " store = zarr.DirectoryStore(baseurl)\n",
+ " grp = zarr.group(store)\n",
+ " print(\"start writing base datset\")\n",
" img.to_zarr(url=os.path.join(baseurl, '0'))\n",
" datasets = [{'path':'0'},]\n",
+ " \n",
" for i in range(nzooms-1):\n",
- " img = img["
+ " j = i + 1\n",
+ " print(f\"Start writing {j} dataset (bin {2**j})\")\n",
+ " img = img[:,:,:,::2,::2]\n",
+ " img.to_zarr(url=os.path.join(baseurl, j))\n",
+ " datasets.append({'path': f'{j}'}) \n",
+ "\n",
+ " grp.attrs['multiscales'] = {\n",
+ " \"multiscales\": [\n",
+ " {\n",
+ " \"datasets\": datasets,\n",
+ " \"name\": os.path.basename(path),\n",
+ " \"type\": \"skip\",\n",
+ " \"version\": \"0.1\"\n",
+ " },\n",
+ "\n",
+ " ]\n",
+ " }\n",
+ " "
]
},
{
"cell_type": "code",
- "execution_count": 3,
+ "execution_count": 5,
"id": "55e2186a-4c4d-4745-972e-791a25fff26b",
"metadata": {},
"outputs": [
@@ -45,148 +68,192 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "Failed to parse XML for the provided file. Error: not well-formed (invalid token): line 1, column 6\n",
- "C:\\Users\\aaristov\\Documents\\nd2shrink\\venv\\lib\\site-packages\\aicsimageio\\aics_image.py:498: PerformanceWarning: Reshaping is producing a large chunk. To accept the large\n",
- "chunk and silence this warning, set the option\n",
- " >>> with dask.config.set(**{'array.slicing.split_large_chunks': False}):\n",
- " ... array.reshape(shape)\n",
- "\n",
- "To avoid creating the large chunks, set the option\n",
- " >>> with dask.config.set(**{'array.slicing.split_large_chunks': True}):\n",
- " ... array.reshape(shape)Explictly passing ``limit`` to ``reshape`` will also silence this warning\n",
- " >>> array.reshape(shape, limit='128 MiB')\n",
- " return self.xarray_dask_data.data\n"
+ "Failed to parse XML for the provided file.\n",
+ "not well-formed (invalid token): line 1, column 6\n",
+ "C:\\Users\\nikon\\miniconda3\\envs\\nd2\\lib\\site-packages\\dask\\array\\core.py:1519: RuntimeWarning: overflow encountered in long_scalars\n",
+ " cbytes = format_bytes(np.prod(self.chunksize) * self.dtype.itemsize)\n"
]
+ },
+ {
+ "data": {
+ "text/html": [
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+ " <tr>\n",
+ " <td>\n",
+ " <table>\n",
+ " <thead>\n",
+ " <tr>\n",
+ " <td> </td>\n",
+ " <th> Array </th>\n",
+ " <th> Chunk </th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " \n",
+ " <tr>\n",
+ " <th> Bytes </th>\n",
+ " <td> 10.02 GiB </td>\n",
+ " <td> -707840896 B </td>\n",
+ " </tr>\n",
+ " \n",
+ " <tr>\n",
+ " <th> Shape </th>\n",
+ " <td> (1, 3, 156, 3900, 2948) </td>\n",
+ " <td> (1, 1, 156, 3900, 2948) </td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th> Count </th>\n",
+ " <td> 21 Tasks </td>\n",
+ " <td> 3 Chunks </td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th> Type </th>\n",
+ " <td> uint16 </td>\n",
+ " <td> numpy.ndarray </td>\n",
+ " </tr>\n",
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+ "text/plain": [
+ "dask.array<transpose, shape=(1, 3, 156, 3900, 2948), dtype=uint16, chunksize=(1, 1, 156, 3900, 2948), chunktype=numpy.ndarray>"
+ ]
+ },
+ "execution_count": 5,
+ "metadata": {},
+ "output_type": "execute_result"
}
],
"source": [
- "img = aicsimageio.imread_dask('Y:/Gustave/Peixoto/image_1/210309_5_Cut.tif')"
+ "img = aicsimageio.imread_dask('Y:/Gustave/Peixoto/image_1/210309_5_Cut.tif')\n",
+ "img"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "id": "1e7774cb-2c6e-4920-a767-6f33eaff0544",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "img = aicsimageio.imread_dask('Y:/Lena/Data/20220111-MIC-resistant/timelapse-30min/0ng-TRITC-19h.nd2')"
]
},
{
"cell_type": "code",
- "execution_count": 12,
- "id": "763c8b11-58ed-45ec-8e45-56e22aa4e5c4",
+ "execution_count": null,
+ "id": "4af272eb-f8ed-4b9c-8d87-95a805d9537a",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
- "Requirement already satisfied: aicsimageio[nd2] in c:\\users\\aaristov\\documents\\nd2shrink\\venv\\lib\\site-packages (4.6.0)\n",
- "Requirement already satisfied: numpy<2,>=1.16 in c:\\users\\aaristov\\documents\\nd2shrink\\venv\\lib\\site-packages (from aicsimageio[nd2]) (1.21.5)\n",
- "Requirement already satisfied: tifffile>=2021.8.30 in c:\\users\\aaristov\\documents\\nd2shrink\\venv\\lib\\site-packages (from aicsimageio[nd2]) (2022.2.9)\n",
- "Requirement already satisfied: wrapt>=1.12 in c:\\users\\aaristov\\documents\\nd2shrink\\venv\\lib\\site-packages (from aicsimageio[nd2]) (1.13.3)\n",
- "Requirement already satisfied: xmlschema in c:\\users\\aaristov\\documents\\nd2shrink\\venv\\lib\\site-packages (from aicsimageio[nd2]) (1.9.2)\n",
- "Requirement already satisfied: lxml<5,>=4.6 in c:\\users\\aaristov\\documents\\nd2shrink\\venv\\lib\\site-packages (from aicsimageio[nd2]) (4.8.0)\n",
- "Requirement already satisfied: zarr<3,>=2.6 in c:\\users\\aaristov\\documents\\nd2shrink\\venv\\lib\\site-packages (from aicsimageio[nd2]) (2.11.0)\n",
- "Requirement already satisfied: dask[array]>=2021.4.1 in c:\\users\\aaristov\\documents\\nd2shrink\\venv\\lib\\site-packages (from aicsimageio[nd2]) (2022.2.0)\n",
- "Requirement already satisfied: xarray>=0.16.1 in c:\\users\\aaristov\\documents\\nd2shrink\\venv\\lib\\site-packages (from aicsimageio[nd2]) (0.21.1)\n",
- "Requirement already satisfied: imagecodecs>=2020.5.30 in c:\\users\\aaristov\\documents\\nd2shrink\\venv\\lib\\site-packages (from aicsimageio[nd2]) (2022.2.22)\n",
- "Requirement already satisfied: fsspec>=2021.4.0 in c:\\users\\aaristov\\documents\\nd2shrink\\venv\\lib\\site-packages (from aicsimageio[nd2]) (2022.2.0)\n",
- "Requirement already satisfied: ome-types>=0.2 in c:\\users\\aaristov\\documents\\nd2shrink\\venv\\lib\\site-packages (from aicsimageio[nd2]) (0.2.10)\n",
- "Collecting nd2[legacy]>=0.2.0\n",
- " Downloading nd2-0.2.0-cp39-cp39-win_amd64.whl (753 kB)\n",
- " ------------------------------------- 753.7/753.7 KB 24.0 MB/s eta 0:00:00\n",
- "Requirement already satisfied: pyyaml>=5.3.1 in c:\\users\\aaristov\\documents\\nd2shrink\\venv\\lib\\site-packages (from dask[array]>=2021.4.1->aicsimageio[nd2]) (6.0)\n",
- "Requirement already satisfied: cloudpickle>=1.1.1 in c:\\users\\aaristov\\documents\\nd2shrink\\venv\\lib\\site-packages (from dask[array]>=2021.4.1->aicsimageio[nd2]) (2.0.0)\n",
- "Requirement already satisfied: packaging>=20.0 in c:\\users\\aaristov\\documents\\nd2shrink\\venv\\lib\\site-packages (from dask[array]>=2021.4.1->aicsimageio[nd2]) (21.3)\n",
- "Requirement already satisfied: toolz>=0.8.2 in c:\\users\\aaristov\\documents\\nd2shrink\\venv\\lib\\site-packages (from dask[array]>=2021.4.1->aicsimageio[nd2]) (0.11.2)\n",
- "Requirement already satisfied: partd>=0.3.10 in c:\\users\\aaristov\\documents\\nd2shrink\\venv\\lib\\site-packages (from dask[array]>=2021.4.1->aicsimageio[nd2]) (1.2.0)\n",
- "Collecting resource-backed-dask-array\n",
- " Downloading resource_backed_dask_array-0.1.0-py2.py3-none-any.whl (8.0 kB)\n",
- "Requirement already satisfied: typing-extensions in c:\\users\\aaristov\\documents\\nd2shrink\\venv\\lib\\site-packages (from nd2[legacy]>=0.2.0->aicsimageio[nd2]) (4.1.1)\n",
- "Collecting wurlitzer\n",
- " Downloading wurlitzer-3.0.2-py3-none-any.whl (7.3 kB)\n",
- "Requirement already satisfied: Pint>=0.15 in c:\\users\\aaristov\\documents\\nd2shrink\\venv\\lib\\site-packages (from ome-types>=0.2->aicsimageio[nd2]) (0.18)\n",
- "Requirement already satisfied: pydantic[email]>=1.0 in c:\\users\\aaristov\\documents\\nd2shrink\\venv\\lib\\site-packages (from ome-types>=0.2->aicsimageio[nd2]) (1.9.0)\n",
- "Requirement already satisfied: pandas>=1.1 in c:\\users\\aaristov\\documents\\nd2shrink\\venv\\lib\\site-packages (from xarray>=0.16.1->aicsimageio[nd2]) (1.4.1)\n",
- "Requirement already satisfied: elementpath<3.0.0,>=2.4.0 in c:\\users\\aaristov\\documents\\nd2shrink\\venv\\lib\\site-packages (from xmlschema->aicsimageio[nd2]) (2.4.0)\n",
- "Requirement already satisfied: asciitree in c:\\users\\aaristov\\documents\\nd2shrink\\venv\\lib\\site-packages (from zarr<3,>=2.6->aicsimageio[nd2]) (0.3.3)\n",
- "Requirement already satisfied: numcodecs>=0.6.4 in c:\\users\\aaristov\\documents\\nd2shrink\\venv\\lib\\site-packages (from zarr<3,>=2.6->aicsimageio[nd2]) (0.9.1)\n",
- "Requirement already satisfied: fasteners in c:\\users\\aaristov\\documents\\nd2shrink\\venv\\lib\\site-packages (from zarr<3,>=2.6->aicsimageio[nd2]) (0.17.3)\n",
- "Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in c:\\users\\aaristov\\documents\\nd2shrink\\venv\\lib\\site-packages (from packaging>=20.0->dask[array]>=2021.4.1->aicsimageio[nd2]) (3.0.7)\n",
- "Requirement already satisfied: python-dateutil>=2.8.1 in c:\\users\\aaristov\\documents\\nd2shrink\\venv\\lib\\site-packages (from pandas>=1.1->xarray>=0.16.1->aicsimageio[nd2]) (2.8.2)\n",
- "Requirement already satisfied: pytz>=2020.1 in c:\\users\\aaristov\\documents\\nd2shrink\\venv\\lib\\site-packages (from pandas>=1.1->xarray>=0.16.1->aicsimageio[nd2]) (2021.3)\n",
- "Requirement already satisfied: locket in c:\\users\\aaristov\\documents\\nd2shrink\\venv\\lib\\site-packages (from partd>=0.3.10->dask[array]>=2021.4.1->aicsimageio[nd2]) (0.2.1)\n",
- "Requirement already satisfied: email-validator>=1.0.3 in c:\\users\\aaristov\\documents\\nd2shrink\\venv\\lib\\site-packages (from pydantic[email]>=1.0->ome-types>=0.2->aicsimageio[nd2]) (1.1.3)\n",
- "Requirement already satisfied: dnspython>=1.15.0 in c:\\users\\aaristov\\documents\\nd2shrink\\venv\\lib\\site-packages (from email-validator>=1.0.3->pydantic[email]>=1.0->ome-types>=0.2->aicsimageio[nd2]) (2.2.0)\n",
- "Requirement already satisfied: idna>=2.0.0 in c:\\users\\aaristov\\documents\\nd2shrink\\venv\\lib\\site-packages (from email-validator>=1.0.3->pydantic[email]>=1.0->ome-types>=0.2->aicsimageio[nd2]) (3.3)\n",
- "Requirement already satisfied: six>=1.5 in c:\\users\\aaristov\\documents\\nd2shrink\\venv\\lib\\site-packages (from python-dateutil>=2.8.1->pandas>=1.1->xarray>=0.16.1->aicsimageio[nd2]) (1.16.0)\n",
- "Installing collected packages: wurlitzer, resource-backed-dask-array, nd2\n",
- "Successfully installed nd2-0.2.0 resource-backed-dask-array-0.1.0 wurlitzer-3.0.2\n"
+ "dask.array<transpose, shape=(39, 1, 25, 7383, 22392), dtype=uint16, chunksize=(1, 1, 1, 7383, 22392), chunktype=numpy.ndarray>\n",
+ "rechunk dask.array<rechunk-merge, shape=(39, 1, 25, 7383, 22392), dtype=uint16, chunksize=(1, 1, 25, 512, 512), chunktype=numpy.ndarray>\n",
+ "Y:/Lena/Data/20220111-MIC-resistant/timelapse-30min/0ng-TRITC-19h.zarr\n",
+ "start writing base datset\n"
]
}
],
"source": [
- "!pip install aicsimageio[nd2]"
+ "convert2zarr(\n",
+ " 'Y:/Lena/Data/20220111-MIC-resistant/timelapse-30min/0ng-TRITC-19h.nd2',\n",
+ " chunksize=(1,1,25,512,512)\n",
+ ")"
]
},
{
"cell_type": "code",
- "execution_count": 16,
- "id": "a9abcdd3-3288-4b84-bf6e-fa9847b68f49",
+ "execution_count": 11,
+ "id": "bdb27aea-e704-4e21-a731-c8584ce8ff50",
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "'dask.array<transpose, shape=(39, 1, 25, 7383, 22392), dtype=uint16, chunksize=(1, 1, 1, 7383, 22392), chunktype=numpy.ndarray>'"
+ ]
+ },
+ "execution_count": 11,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
"source": [
- "img = aicsimageio.AICSImage(\"Y:/Lena/Data/20211207-control-timelapse/00ng-TRITC_30min.nd2\")"
+ "img"
]
},
{
"cell_type": "code",
- "execution_count": 21,
- "id": "9b252cd8-4d63-4dc1-818c-a1e665008ba6",
+ "execution_count": 16,
+ "id": "a9abcdd3-3288-4b84-bf6e-fa9847b68f49",
"metadata": {},
"outputs": [],
"source": [
- "v = napari.Viewer()"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 20,
- "id": "fa94292a-f749-496e-aeed-03035fcb37b6",
- "metadata": {},
- "outputs": [
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "Traceback (most recent call last):\n",
- " File \"C:\\Users\\aaristov\\Documents\\nd2shrink\\venv\\lib\\site-packages\\napari\\plugins\\io.py\", line 108, in read_data_with_plugins\n",
- " layer_data = reader(path) # try to read data\n",
- "TypeError: 'NoneType' object is not callable\n",
- "\n",
- "During handling of the above exception, another exception occurred:\n",
- "\n",
- "Traceback (most recent call last):\n",
- " File \"C:\\Program Files\\WindowsApps\\PythonSoftwareFoundation.Python.3.9_3.9.2800.0_x64__qbz5n2kfra8p0\\lib\\runpy.py\", line 197, in _run_module_as_main\n",
- " return _run_code(code, main_globals, None,\n",
- " File \"C:\\Program Files\\WindowsApps\\PythonSoftwareFoundation.Python.3.9_3.9.2800.0_x64__qbz5n2kfra8p0\\lib\\runpy.py\", line 87, in _run_code\n",
- " exec(code, run_globals)\n",
- " File \"C:\\Users\\aaristov\\Documents\\nd2shrink\\venv\\Scripts\\napari.exe\\__main__.py\", line 7, in <module>\n",
- " File \"C:\\Users\\aaristov\\Documents\\nd2shrink\\venv\\lib\\site-packages\\napari\\__main__.py\", line 449, in main\n",
- " _run()\n",
- " File \"C:\\Users\\aaristov\\Documents\\nd2shrink\\venv\\lib\\site-packages\\napari\\__main__.py\", line 314, in _run\n",
- " viewer = view_path( # noqa: F841\n",
- " File \"C:\\Users\\aaristov\\Documents\\nd2shrink\\venv\\lib\\site-packages\\napari\\view_layers.py\", line 178, in view_path\n",
- " return _make_viewer_then('open', args, kwargs)\n",
- " File \"C:\\Users\\aaristov\\Documents\\nd2shrink\\venv\\lib\\site-packages\\napari\\view_layers.py\", line 126, in _make_viewer_then\n",
- " method(*args, **kwargs)\n",
- " File \"C:\\Users\\aaristov\\Documents\\nd2shrink\\venv\\lib\\site-packages\\napari\\components\\viewer_model.py\", line 907, in open\n",
- " self._add_layers_with_plugins(\n",
- " File \"C:\\Users\\aaristov\\Documents\\nd2shrink\\venv\\lib\\site-packages\\napari\\components\\viewer_model.py\", line 952, in _add_layers_with_plugins\n",
- " layer_data, hookimpl = read_data_with_plugins(\n",
- " File \"C:\\Users\\aaristov\\Documents\\nd2shrink\\venv\\lib\\site-packages\\napari\\plugins\\io.py\", line 111, in read_data_with_plugins\n",
- " raise PluginCallError(result.implementation, cause=exc)\n",
- " File \"C:\\Users\\aaristov\\Documents\\nd2shrink\\venv\\lib\\site-packages\\napari_plugin_engine\\exceptions.py\", line 197, in __init__\n",
- " plugin = hook_implementation.plugin\n",
- "AttributeError: 'NoneType' object has no attribute 'plugin'\n"
- ]
- }
- ],
- "source": [
- "!napari \"Y:/Lena/Data/20211207-control-timelapse/00ng-TRITC_30min.nd2\""
+ "img = aicsimageio.AICSImage(\"Y:/Lena/Data/20211207-control-timelapse/00ng-TRITC_30min.nd2\")"
]
},
{
@@ -972,30 +1039,14 @@
{
"cell_type": "code",
"execution_count": 58,
- "id": "c7428267-a9b8-4e93-b72f-0d2026de28a1",
- "metadata": {},
- "outputs": [],
- "source": [
- "store = zarr.DirectoryStore('/home/aaristov/Downloads/Gustave_Peixoto_image_1_210309_5_Cut_2.zarr')"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 68,
- "id": "c697016e-fe85-4213-b262-7be953e251c3",
- "metadata": {},
- "outputs": [],
- "source": [
- "grp = zarr.group(store)"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 71,
- "id": "07b014e4-6273-4222-8c24-a431c826bd03",
+ "id": "7920ae04-f76f-4eb5-9216-e1f4d73de0c7",
"metadata": {},
"outputs": [],
"source": [
+ "store = zarr.DirectoryStore('/home/aaristov/Downloads/Gustave_Peixoto_image_1_210309_5_Cut_2.zarr')\n",
+ "\n",
+ "grp = zarr.group(store)\n",
+ "\n",
"grp.attrs['multiscales'] = {\n",
" \"multiscales\": [\n",
" {\n",
@@ -1057,126 +1108,6 @@
"img8.to_zarr(path.join(baseurl, '3'))\n"
]
},
- {
- "cell_type": "code",
- "execution_count": 5,
- "id": "a0c35aa5-9dae-4a90-a3a9-aeb0a8fbe80d",
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Requirement already satisfied: napari in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (0.4.13)\n",
- "Collecting napari\n",
- " Downloading napari-0.4.14-py3-none-any.whl (2.5 MB)\n",
- "\u001b[K |████████████████████████████████| 2.5 MB 30.0 MB/s eta 0:00:01\n",
- "\u001b[?25hRequirement already satisfied: numpydoc>=0.9.2 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from napari) (1.1.0)\n",
- "Requirement already satisfied: scipy>=1.4.0 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from napari) (1.7.3)\n",
- "Requirement already satisfied: npe2>=0.1.1 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from napari) (0.1.1)\n",
- "Requirement already satisfied: typing-extensions in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from napari) (3.10.0.2)\n",
- "Requirement already satisfied: pandas>=1.1.0 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from napari) (1.1.0)\n",
- "Requirement already satisfied: pydantic>=1.8.1 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from napari) (1.8.2)\n",
- "Requirement already satisfied: imageio!=2.11.0,>=2.5.0 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from napari) (2.8.0)\n",
- "Requirement already satisfied: toolz>=0.10.0 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from napari) (0.11.1)\n",
- "Requirement already satisfied: magicgui>=0.3.3 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from napari) (0.3.3)\n",
- "Requirement already satisfied: appdirs>=1.4.4 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from napari) (1.4.4)\n",
- "Requirement already satisfied: napari-console>=0.0.4 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from napari) (0.0.4)\n",
- "Requirement already satisfied: Pillow!=7.1.0,!=7.1.1 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from napari) (8.4.0)\n",
- "Requirement already satisfied: certifi>=2018.1.18 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from napari) (2021.10.8)\n",
- "Requirement already satisfied: PyOpenGL>=3.1.0 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from napari) (3.1.5)\n",
- "Requirement already satisfied: vispy>=0.9.4 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from napari) (0.9.4)\n",
- "Requirement already satisfied: numpy>=1.18.5 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from napari) (1.21.2)\n",
- "Requirement already satisfied: tqdm>=4.56.0 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from napari) (4.62.3)\n",
- "Requirement already satisfied: wrapt>=1.11.1 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from napari) (1.13.3)\n",
- "Requirement already satisfied: cachey>=0.2.1 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from napari) (0.2.1)\n",
- "Requirement already satisfied: qtpy>=1.7.0 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from napari) (1.11.2)\n",
- "Requirement already satisfied: napari-svg>=0.1.4 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from napari) (0.1.6)\n",
- "Requirement already satisfied: tifffile>=2020.2.16 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from napari) (2021.8.30)\n",
- "Requirement already satisfied: superqt>=0.2.5 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from napari) (0.2.5.post1)\n",
- "Requirement already satisfied: dask[array]!=2.28.0,>=2.15.0 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from napari) (2021.9.1)\n",
- "Requirement already satisfied: psutil>=5.0 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from napari) (5.8.0)\n",
- "Requirement already satisfied: napari-plugin-engine>=0.1.9 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from napari) (0.2.0)\n",
- "Requirement already satisfied: pint>=0.17 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from napari) (0.17)\n",
- "Requirement already satisfied: jsonschema>=3.2.0 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from napari) (3.2.0)\n",
- "Requirement already satisfied: PyYAML>=5.1 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from napari) (6.0)\n",
- "Requirement already satisfied: heapdict in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from cachey>=0.2.1->napari) (1.0.1)\n",
- "Requirement already satisfied: fsspec>=0.6.0 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from dask[array]!=2.28.0,>=2.15.0->napari) (2021.9.0)\n",
- "Requirement already satisfied: packaging>=20.0 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from dask[array]!=2.28.0,>=2.15.0->napari) (21.3)\n",
- "Requirement already satisfied: cloudpickle>=1.1.1 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from dask[array]!=2.28.0,>=2.15.0->napari) (2.0.0)\n",
- "Requirement already satisfied: partd>=0.3.10 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from dask[array]!=2.28.0,>=2.15.0->napari) (1.2.0)\n",
- "Requirement already satisfied: pyrsistent>=0.14.0 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from jsonschema>=3.2.0->napari) (0.18.0)\n",
- "Requirement already satisfied: setuptools in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from jsonschema>=3.2.0->napari) (58.0.4)\n",
- "Requirement already satisfied: attrs>=17.4.0 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from jsonschema>=3.2.0->napari) (21.4.0)\n",
- "Requirement already satisfied: six>=1.11.0 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from jsonschema>=3.2.0->napari) (1.16.0)\n",
- "Requirement already satisfied: docstring-parser in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from magicgui>=0.3.3->napari) (0.12)\n",
- "Requirement already satisfied: psygnal>=0.2.0 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from magicgui>=0.3.3->napari) (0.2.0)\n",
- "Requirement already satisfied: qtconsole!=4.7.6,>=4.5.1 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from napari-console>=0.0.4->napari) (5.1.1)\n",
- "Requirement already satisfied: IPython>=7.7.0 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from napari-console>=0.0.4->napari) (7.31.1)\n",
- "Requirement already satisfied: ipykernel>=5.2.0 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from napari-console>=0.0.4->napari) (6.4.1)\n",
- "Requirement already satisfied: jupyter-client<8.0 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from ipykernel>=5.2.0->napari-console>=0.0.4->napari) (7.1.2)\n",
- "Requirement already satisfied: traitlets<6.0,>=4.1.0 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from ipykernel>=5.2.0->napari-console>=0.0.4->napari) (5.1.1)\n",
- "Requirement already satisfied: ipython-genutils in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from ipykernel>=5.2.0->napari-console>=0.0.4->napari) (0.2.0)\n",
- "Requirement already satisfied: matplotlib-inline<0.2.0,>=0.1.0 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from ipykernel>=5.2.0->napari-console>=0.0.4->napari) (0.1.2)\n",
- "Requirement already satisfied: debugpy<2.0,>=1.0.0 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from ipykernel>=5.2.0->napari-console>=0.0.4->napari) (1.5.1)\n",
- "Requirement already satisfied: tornado<7.0,>=4.2 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from ipykernel>=5.2.0->napari-console>=0.0.4->napari) (6.1)\n",
- "Requirement already satisfied: pygments in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from IPython>=7.7.0->napari-console>=0.0.4->napari) (2.11.2)\n",
- "Requirement already satisfied: prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from IPython>=7.7.0->napari-console>=0.0.4->napari) (3.0.20)\n",
- "Requirement already satisfied: backcall in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from IPython>=7.7.0->napari-console>=0.0.4->napari) (0.2.0)\n",
- "Requirement already satisfied: pexpect>4.3 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from IPython>=7.7.0->napari-console>=0.0.4->napari) (4.8.0)\n",
- "Requirement already satisfied: pickleshare in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from IPython>=7.7.0->napari-console>=0.0.4->napari) (0.7.5)\n",
- "Requirement already satisfied: jedi>=0.16 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from IPython>=7.7.0->napari-console>=0.0.4->napari) (0.18.1)\n",
- "Requirement already satisfied: decorator in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from IPython>=7.7.0->napari-console>=0.0.4->napari) (5.1.1)\n",
- "Requirement already satisfied: parso<0.9.0,>=0.8.0 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from jedi>=0.16->IPython>=7.7.0->napari-console>=0.0.4->napari) (0.8.3)\n",
- "Requirement already satisfied: entrypoints in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from jupyter-client<8.0->ipykernel>=5.2.0->napari-console>=0.0.4->napari) (0.3)\n",
- "Requirement already satisfied: jupyter-core>=4.6.0 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from jupyter-client<8.0->ipykernel>=5.2.0->napari-console>=0.0.4->napari) (4.9.1)\n",
- "Requirement already satisfied: python-dateutil>=2.1 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from jupyter-client<8.0->ipykernel>=5.2.0->napari-console>=0.0.4->napari) (2.8.2)\n",
- "Requirement already satisfied: pyzmq>=13 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from jupyter-client<8.0->ipykernel>=5.2.0->napari-console>=0.0.4->napari) (22.3.0)\n",
- "Requirement already satisfied: nest-asyncio>=1.5 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from jupyter-client<8.0->ipykernel>=5.2.0->napari-console>=0.0.4->napari) (1.5.1)\n",
- "Requirement already satisfied: typer in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from npe2>=0.1.1->napari) (0.4.0)\n",
- "Requirement already satisfied: pytomlpp in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from npe2>=0.1.1->napari) (1.0.10)\n",
- "Requirement already satisfied: intervaltree in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from npe2>=0.1.1->napari) (3.1.0)\n",
- "Requirement already satisfied: Jinja2>=2.3 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from numpydoc>=0.9.2->napari) (3.0.2)\n",
- "Requirement already satisfied: sphinx>=1.6.5 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from numpydoc>=0.9.2->napari) (4.2.0)\n",
- "Requirement already satisfied: MarkupSafe>=2.0 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from Jinja2>=2.3->numpydoc>=0.9.2->napari) (2.0.1)\n",
- "Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from packaging>=20.0->dask[array]!=2.28.0,>=2.15.0->napari) (3.0.4)\n",
- "Requirement already satisfied: pytz>=2017.2 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from pandas>=1.1.0->napari) (2021.3)\n",
- "Requirement already satisfied: locket in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from partd>=0.3.10->dask[array]!=2.28.0,>=2.15.0->napari) (0.2.1)\n",
- "Requirement already satisfied: ptyprocess>=0.5 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from pexpect>4.3->IPython>=7.7.0->napari-console>=0.0.4->napari) (0.7.0)\n",
- "Requirement already satisfied: wcwidth in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0->IPython>=7.7.0->napari-console>=0.0.4->napari) (0.2.5)\n",
- "Requirement already satisfied: sphinxcontrib-htmlhelp>=2.0.0 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from sphinx>=1.6.5->numpydoc>=0.9.2->napari) (2.0.0)\n",
- "Requirement already satisfied: requests>=2.5.0 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from sphinx>=1.6.5->numpydoc>=0.9.2->napari) (2.27.1)\n",
- "Requirement already satisfied: sphinxcontrib-jsmath in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from sphinx>=1.6.5->numpydoc>=0.9.2->napari) (1.0.1)\n",
- "Requirement already satisfied: docutils<0.18,>=0.14 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from sphinx>=1.6.5->numpydoc>=0.9.2->napari) (0.17.1)\n",
- "Requirement already satisfied: sphinxcontrib-devhelp in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from sphinx>=1.6.5->numpydoc>=0.9.2->napari) (1.0.2)\n",
- "Requirement already satisfied: sphinxcontrib-applehelp in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from sphinx>=1.6.5->numpydoc>=0.9.2->napari) (1.0.2)\n",
- "Requirement already satisfied: sphinxcontrib-qthelp in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from sphinx>=1.6.5->numpydoc>=0.9.2->napari) (1.0.3)\n",
- "Requirement already satisfied: alabaster<0.8,>=0.7 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from sphinx>=1.6.5->numpydoc>=0.9.2->napari) (0.7.12)\n",
- "Requirement already satisfied: snowballstemmer>=1.1 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from sphinx>=1.6.5->numpydoc>=0.9.2->napari) (2.1.0)\n",
- "Requirement already satisfied: babel>=1.3 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from sphinx>=1.6.5->numpydoc>=0.9.2->napari) (2.9.1)\n",
- "Requirement already satisfied: imagesize in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from sphinx>=1.6.5->numpydoc>=0.9.2->napari) (1.2.0)\n",
- "Requirement already satisfied: sphinxcontrib-serializinghtml>=1.1.5 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from sphinx>=1.6.5->numpydoc>=0.9.2->napari) (1.1.5)\n",
- "Requirement already satisfied: idna<4,>=2.5 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from requests>=2.5.0->sphinx>=1.6.5->numpydoc>=0.9.2->napari) (3.3)\n",
- "Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from requests>=2.5.0->sphinx>=1.6.5->numpydoc>=0.9.2->napari) (1.26.8)\n",
- "Requirement already satisfied: charset-normalizer~=2.0.0 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from requests>=2.5.0->sphinx>=1.6.5->numpydoc>=0.9.2->napari) (2.0.7)\n",
- "Requirement already satisfied: kiwisolver in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from vispy>=0.9.4->napari) (1.3.2)\n",
- "Requirement already satisfied: freetype-py in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from vispy>=0.9.4->napari) (2.2.0)\n",
- "Requirement already satisfied: hsluv in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from vispy>=0.9.4->napari) (5.0.2)\n",
- "Requirement already satisfied: sortedcontainers<3.0,>=2.0 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from intervaltree->npe2>=0.1.1->napari) (2.4.0)\n",
- "Requirement already satisfied: click<9.0.0,>=7.1.1 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from typer->npe2>=0.1.1->napari) (7.1.2)\n",
- "Installing collected packages: napari\n",
- " Attempting uninstall: napari\n",
- " Found existing installation: napari 0.4.13\n",
- " Uninstalling napari-0.4.13:\n",
- " Successfully uninstalled napari-0.4.13\n",
- "Successfully installed napari-0.4.14\n"
- ]
- }
- ],
- "source": [
- "!pip install -U napari"
- ]
- },
{
"cell_type": "code",
"execution_count": 6,
@@ -1222,7 +1153,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.9.10"
+ "version": "3.8.12"
}
},
"nbformat": 4,