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WhiteDataReader
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@yasinthanvickneswaran
yasinthanvickneswaran committed Feb 21, 2024
1 parent 8bbe666 commit 3dbf9c8
Showing 1 changed file with 137 additions and 28 deletions.
165 changes: 137 additions & 28 deletions examples/test/Comparison.ipynb
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"cells": [
{
"cell_type": "code",
"execution_count": 1,
"execution_count": 3,
"id": "481d3c70-313a-4979-8475-d4a0089a8a0b",
"metadata": {
"tags": []
Expand All @@ -16,52 +16,113 @@
"****** Importing dataset SpreadsheetData using c302.SpreadsheetDataReader ******\n",
"c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/CElegansNeuronTables.xls\n",
"c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/CElegansNeuronTables.xls\n",
"c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/CElegansNeuronTables.xls\n",
"c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/CElegansNeuronTables.xls\n",
"c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/CElegansNeuronTables.xls\n",
"c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/CElegansNeuronTables.xls\n",
"c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/CElegansNeuronTables.xls\n",
"c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/CElegansNeuronTables.xls\n",
"c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/CElegansNeuronTables.xls\n",
"c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/CElegansNeuronTables.xls\n",
"c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/CElegansNeuronTables.xls\n",
"c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/CElegansNeuronTables.xls\n",
"\n",
"****** Importing dataset UpdSpreadsheetData using c302.UpdatedSpreadsheetDataReader ******\n",
"c302 >>> Opened file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/herm_full_edgelist.csv\n",
"c302 >>> Opened file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/herm_full_edgelist.csv\n",
"c302 >>> Opened file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/herm_full_edgelist.csv\n",
"c302 >>> Opened file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/herm_full_edgelist.csv\n",
"\n",
"****** Importing dataset UpdSpreadsheetData2 using c302.UpdatedSpreadsheetDataReader2 ******\n",
"c302 >>> Opened file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/herm_full_edgelist_MODIFIED.csv\n",
"c302 >>> Opened file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/herm_full_edgelist_MODIFIED.csv\n",
"c302 >>> Opened file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/herm_full_edgelist_MODIFIED.csv\n",
"c302 >>> Opened file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/herm_full_edgelist_MODIFIED.csv\n",
"\n",
"****** Importing dataset OpenWorm using c302.OpenWormReader ******\n",
"c302 >>> Initialising OpenWormReader\n",
"c302 >>> Total cells 302 (300 with connections)\n",
"c302 >>> Total connections found 5805 \n",
"c302 >>> Total cells 397 (254 with connections)\n",
"c302 >>> Total connections found 926 \n",
"c302 >>> Total cells 397 (254 with connections)\n",
"c302 >>> Total connections found 926 \n",
"c302 >>> Total cells 397 (254 with connections)\n",
"c302 >>> Total connections found 926 \n",
"c302 >>> Total cells 397 (254 with connections)\n",
"c302 >>> Total connections found 926 \n",
"c302 >>> Total cells 397 (254 with connections)\n",
"c302 >>> Total connections found 926 \n",
"c302 >>> Total cells 397 (254 with connections)\n",
"c302 >>> Total connections found 926 \n",
"c302 >>> Total cells 397 (254 with connections)\n",
"c302 >>> Total connections found 926 \n",
"c302 >>> Total cells 397 (254 with connections)\n",
"c302 >>> Total connections found 926 \n",
"c302 >>> Total cells 397 (254 with connections)\n",
"c302 >>> Total connections found 926 \n",
"c302 >>> Total cells 397 (254 with connections)\n",
"c302 >>> Total connections found 926 \n",
"c302 >>> Total cells 397 (254 with connections)\n",
"c302 >>> Total connections found 926 \n",
"c302 >>> Total cells 397 (254 with connections)\n",
"c302 >>> Total connections found 926 \n",
"c302 >>> Total cells 397 (254 with connections)\n",
"c302 >>> Total connections found 926 \n",
"c302 >>> Total cells 397 (254 with connections)\n",
"c302 >>> Total connections found 926 \n",
"c302 >>> Total cells 397 (254 with connections)\n",
"c302 >>> Total connections found 926 \n",
"c302 >>> Total cells 397 (254 with connections)\n",
"c302 >>> Total connections found 926 \n",
"c302 >>> Total cells 397 (254 with connections)\n",
"c302 >>> Total connections found 926 \n",
"c302 >>> Total cells 397 (254 with connections)\n",
"c302 >>> Total connections found 926 \n",
"c302 >>> Total cells 397 (254 with connections)\n",
"c302 >>> Total connections found 926 \n",
"c302 >>> Total cells 397 (254 with connections)\n",
"c302 >>> Total connections found 926 \n",
"c302 >>> Total cells 397 (254 with connections)\n",
"c302 >>> Total connections found 926 \n",
"c302 >>> Total cells 397 (254 with connections)\n",
"c302 >>> Total connections found 926 \n",
"c302 >>> Total cells 397 (254 with connections)\n",
"c302 >>> Total connections found 926 \n",
"\n",
"****** Importing dataset WormNeuroAtlas using c302.WormNeuroAtlasReader ******\n",
"*This version of the NeuroAtlas does not include the CAN neurons. This will be fixed soon.\n",
"*In loading the anatomical connectome, the following conventions are used to allow for its comparison with the other datasets: AWCL->AWCOFF and AWCR->AWCON\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\wormneuroatlas\\WormBase.py:52: UserWarning: Wormbase.org updated its database to a new version (WS291). The version of Worm Neuro Atlas that you are using has been built for the wormbase database version WS287. To ensure reproducible results, upgrade Worm Neuro Atlas with `python -m pip install --upgrade wormneuroatlas` If this warning persists after upgrading, let the developers know by opening an issue here: https://github.com/francescorandi/wormneuroatlas/issues. NOTE: You can still use Worm Neuro Atlas in the meantime. The metadata accessible via wormneuroatlas.WormBase.get_metadata() and wormneuroatlas.NeuroAtlas.get_metadata() contain the version of wormbase that you are currently using, so make sure you save the metadata alongside your results. \n",
" warnings.warn(w)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"c302 >>> Initialising WormNeuroAtlasReader\n",
"\n",
"****** Importing dataset Varshney using c302.VarshneyDataReader ******\n",
"c302 >>> Opened the Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/NeuronConnectFormatted.xlsx\n",
"c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/NeuronConnectFormatted.xlsx\n",
"c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/NeuronConnectFormatted.xlsx\n",
"\n",
"****** Importing dataset Witvliet(1) using c302.W_SpreadsheetDataReader ******\n",
"c302 >>> Opened Excel file..: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/witvliet_2020_7.xlsx\n",
"c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/witvliet_2020_7.xlsx\n",
"c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/witvliet_2020_7.xlsx\n",
"\n",
"****** Importing dataset Witvliet(2) using c302.W_SpreadsheetDataReader ******\n",
"c302 >>> Opened Excel file..: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/witvliet_2020_8.xlsx\n",
"c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/witvliet_2020_8.xlsx\n"
"c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/witvliet_2020_8.xlsx\n",
"c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/witvliet_2020_8.xlsx\n",
"\n",
"****** Importing dataset White(A) using c302.WhiteDataReader ******\n",
"c302 >>> Opened file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/aconnectome_white_1986_A.csv\n",
"c302 >>> Opened file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/aconnectome_white_1986_A.csv\n",
"c302 >>> Opened file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/aconnectome_white_1986_A.csv\n",
"\n",
"****** Importing dataset White(L4) using c302.WhiteDataReader ******\n",
"c302 >>> Opened file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/aconnectome_white_1986_L4.csv\n",
"c302 >>> Opened file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/aconnectome_white_1986_L4.csv\n",
"c302 >>> Opened file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/aconnectome_white_1986_L4.csv\n",
"\n",
"****** Importing dataset White(Whole) using c302.WhiteDataReader ******\n",
"c302 >>> Opened file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/aconnectome_white_1986_whole.csv\n",
"c302 >>> Opened file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/aconnectome_white_1986_whole.csv\n",
"c302 >>> Opened file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/aconnectome_white_1986_whole.csv\n",
"c302 >>> Opened file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/aconnectome_white_1986_whole.csv\n"
]
}
],
Expand All @@ -80,23 +141,36 @@
" \"WormNeuroAtlas\": \"c302.WormNeuroAtlasReader\",\n",
" \"Varshney\": \"c302.VarshneyDataReader\",\n",
" \"Witvliet(1)\": \"c302.W_SpreadsheetDataReader\",\n",
" \"Witvliet(2)\": \"c302.W_SpreadsheetDataReader\"}\n",
" \"Witvliet(2)\": \"c302.W_SpreadsheetDataReader\",\n",
" \"White(A)\": \"c302.WhiteDataReader\",\n",
" \"White(L4)\": \"c302.WhiteDataReader\",\n",
" \"White(Whole)\": \"c302.WhiteDataReader\"}\n",
"\n",
"\n",
"for name, reader in readers.items():\n",
"\n",
" print(\"\\n****** Importing dataset %s using %s ******\"% (name, reader))\n",
" \n",
" if name == \"Witvliet(1)\" or name == \"Witvliet(2)\":\n",
" if name == \"Witvliet(1)\":\n",
" if name == \"Witvliet(1)\":\n",
" exec(f\"from {reader} import WitvlietDataReader1\")\n",
" data_reader_instance = eval(f\"WitvlietDataReader1\")\n",
" cells, neuron_conns = data_reader_instance.read_data(include_nonconnected_cells=True)\n",
" elif name == \"Witvliet(2)\":\n",
" elif name == \"Witvliet(2)\":\n",
" exec(f\"from {reader} import WitvlietDataReader2\")\n",
" data_reader_instance = eval(f\"WitvlietDataReader2\")\n",
" cells, neuron_conns = data_reader_instance.read_data(include_nonconnected_cells=True)\n",
"\n",
" elif name == \"White(A)\":\n",
" exec(f\"from {reader} import White_A\")\n",
" data_reader_instance = eval(f\"White_A\")\n",
" cells, neuron_conns = data_reader_instance.read_data(include_nonconnected_cells=True)\n",
" elif name == \"White(L4)\":\n",
" exec(f\"from {reader} import White_L4\")\n",
" data_reader_instance = eval(f\"White_L4\")\n",
" cells, neuron_conns = data_reader_instance.read_data(include_nonconnected_cells=True)\n",
" elif name == \"White(Whole)\":\n",
" exec(f\"from {reader} import White_whole\")\n",
" data_reader_instance = eval(f\"White_whole\")\n",
" cells, neuron_conns = data_reader_instance.read_data(include_nonconnected_cells=True)\n",
" else:\n",
" exec(\"from %s import read_data, read_muscle_data\"%reader)\n",
" cells, neuron_conns = read_data(include_nonconnected_cells=True)\n",
Expand All @@ -116,7 +190,6 @@
" for nts in sorted(neuron_nts.keys()):\n",
" nts_info+='%s (%i)<br/>'%(nts, neuron_nts[nts])\n",
"\n",
" if name == \"Witvliet(1)\" or name == \"Witvliet(2)\":\n",
" if name == \"Witvliet(1)\":\n",
" exec(f\"from {reader} import WitvlietDataReader1\")\n",
" data_reader_instance = eval(f\"WitvlietDataReader1\")\n",
Expand All @@ -125,8 +198,20 @@
" exec(f\"from {reader} import WitvlietDataReader2\")\n",
" data_reader_instance = eval(f\"WitvlietDataReader2\")\n",
" neurons2muscles, muscles, muscle_conns = data_reader_instance.read_muscle_data()\n",
" else:\n",
" neurons2muscles, muscles, muscle_conns = read_muscle_data()\n",
" elif name == \"White(A)\":\n",
" exec(f\"from {reader} import White_A\")\n",
" data_reader_instance = eval(f\"White_A\")\n",
" neurons2muscles, muscles, muscle_conns = data_reader_instance.read_muscle_data()\n",
" elif name == \"White(L4)\":\n",
" exec(f\"from {reader} import White_L4\")\n",
" data_reader_instance = eval(f\"White_L4\")\n",
" neurons2muscles, muscles, muscle_conns = data_reader_instance.read_muscle_data()\n",
" elif name == \"White(Whole)\":\n",
" exec(f\"from {reader} import White_whole\")\n",
" data_reader_instance = eval(f\"White_whole\")\n",
" neurons2muscles, muscles, muscle_conns = data_reader_instance.read_muscle_data()\n",
" else:\n",
" neurons2muscles, muscles, muscle_conns = read_muscle_data()\n",
" \n",
" \n",
" muscle_nts = {}\n",
Expand Down Expand Up @@ -156,7 +241,7 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 4,
"id": "2308051a-0a24-44db-a481-fc0d0f2af4fb",
"metadata": {
"tags": []
Expand All @@ -177,6 +262,9 @@
" <th>Varshney</th>\n",
" <th>Witvliet(1)</th>\n",
" <th>Witvliet(2)</th>\n",
" <th>White(A)</th>\n",
" <th>White(L4)</th>\n",
" <th>White(Whole)</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
Expand All @@ -190,6 +278,9 @@
" <td>279</td>\n",
" <td>225</td>\n",
" <td>222</td>\n",
" <td>191</td>\n",
" <td>185</td>\n",
" <td>311</td>\n",
" </tr>\n",
" <tr>\n",
" <td>Num Muscles</td>\n",
Expand All @@ -201,6 +292,9 @@
" <td>1</td>\n",
" <td>32</td>\n",
" <td>32</td>\n",
" <td>32</td>\n",
" <td>32</td>\n",
" <td>0</td>\n",
" </tr>\n",
" <tr>\n",
" <td>Num N->N conns</td>\n",
Expand All @@ -212,6 +306,9 @@
" <td>6264</td>\n",
" <td>2493</td>\n",
" <td>2496</td>\n",
" <td>1694</td>\n",
" <td>1593</td>\n",
" <td>2961</td>\n",
" </tr>\n",
" <tr>\n",
" <td>Num N with ->M</td>\n",
Expand All @@ -223,6 +320,9 @@
" <td>115</td>\n",
" <td>58</td>\n",
" <td>47</td>\n",
" <td>38</td>\n",
" <td>38</td>\n",
" <td>0</td>\n",
" </tr>\n",
" <tr>\n",
" <td>Num N->M conns</td>\n",
Expand All @@ -234,6 +334,9 @@
" <td>153</td>\n",
" <td>230</td>\n",
" <td>216</td>\n",
" <td>205</td>\n",
" <td>176</td>\n",
" <td>0</td>\n",
" </tr>\n",
" <tr>\n",
" <td>N neurotransmitters</td>\n",
Expand All @@ -245,6 +348,9 @@
" <td>Chemical_Synapse (5233)<br/>Generic_GJ (1031)<br/></td>\n",
" <td>Chemical_Synapse (2202)<br/>Generic_GJ (291)<br/></td>\n",
" <td>Chemical_Synapse (2186)<br/>Generic_GJ (310)<br/></td>\n",
" <td>Acetylcholine (1424)<br/>Generic_GJ (270)<br/></td>\n",
" <td>Acetylcholine (1304)<br/>Generic_GJ (289)<br/></td>\n",
" <td>Acetylcholine (2333)<br/>GABA (53)<br/>Generic_GJ (575)<br/></td>\n",
" </tr>\n",
" <tr>\n",
" <td>M neurotransmitters</td>\n",
Expand All @@ -256,6 +362,9 @@
" <td>Chemical_Synapse (153)<br/></td>\n",
" <td>Chemical_Synapse (230)<br/></td>\n",
" <td>Chemical_Synapse (216)<br/></td>\n",
" <td>Acetylcholine (205)<br/></td>\n",
" <td>Acetylcholine (176)<br/></td>\n",
" <td></td>\n",
" </tr>\n",
" </tbody>\n",
"</table>"
Expand All @@ -264,7 +373,7 @@
"<IPython.core.display.HTML object>"
]
},
"execution_count": 2,
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
Expand Down

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