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mmMapPlot2 in __init__
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Former-commit-id: b0c8f56
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@cudmore
cudmore committed Mar 19, 2018
1 parent a26e166 commit bdb8b7f
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4 changes: 2 additions & 2 deletions app/mmserver.py
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Expand Up @@ -38,8 +38,8 @@
import redis
import pickle

import pymapmanager
print(' mmserver: pymapmanager.__version__:', pymapmanager.__version__)
#import pymapmanager
#print(' mmserver: pymapmanager.__version__:', pymapmanager.__version__)

from pymapmanager import mmMap, mmUtil

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373 changes: 230 additions & 143 deletions examples/.ipynb_checkpoints/b - dynamics-checkpoint.ipynb
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76 changes: 31 additions & 45 deletions examples/a-plotting-annotations.ipynb
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373 changes: 230 additions & 143 deletions examples/b - dynamics.ipynb
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22 changes: 11 additions & 11 deletions examples/c - Intensity Analysis.ipynb
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24 changes: 14 additions & 10 deletions examples/d - segment statistics.ipynb
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Expand Up @@ -16,7 +16,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"map rr30a loaded in 0.45 seconds.\n"
"map rr30a loaded in 0.46 seconds.\n"
]
}
],
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"<table border=\"1\" class=\"dataframe\">\n",
Expand Down Expand Up @@ -154,14 +158,14 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"['Idx', 'roiType', 'roiTypeNum', 'x', 'y', 'z', 'channel', 'groupID', 'parentID', 'cPnt', 'sDist', 'pDist', 'cAuto', 'cAngle', 'cLine', 'cLineNum', 'cx', 'cy', 'cz', 'cDate', 'cTime', 'mDate', 'mTime', 'cSeconds', 'mSeconds', 'userName', 'note', 'edgeList', 'isDirty', 'isBad', 'dynBad', 'intBad', 'progType', 'madeFrom', 'analParam', 'analResult1', 'analResult2', 'analResult3', 'analResult4', 'user1', 'user2', 'user3', 'userBool1', 'userBool2', 'userBool3', 'userType', 'bSpineMap', 'bSpineIdx', 'error', 'warning', 'Unnamed: 50', 'mapName', 'mapSession', 'next', 'nexttp', 'prev', 'prevtp', 'runIdx', 'days', 'sessCond', 'mapCond', 'isAdd', 'isSub', 'isTransient', 'idx_int1', 'x_int1', 'y_int1', 'z_int1', 'sLen2d_int1', 'sLen3d_int1', 'intmSeconds_int1', 'isDirty_int1', 'intBad_int1', 'intManual_int1', 'spineWidth_int1', 'extendHead_int1', 'extendTail_int1', 'scaleRadius_int1', 'zPlusMinus_int1', 'sSum_int1', 'sMean_int1', 'sSD_int1', 'sN_int1', 'sbSum_int1', 'sbMean_int1', 'sbSD_int1', 'sbN_int1', 'sbxyManual_int1', 'sbxPos_int1', 'sbyPos_int1', 'dSum_int1', 'dMean_int1', 'dSD_int1', 'dN_int1', 'dPlus_int1', 'dMinus_int1', 'dbSum_int1', 'dbMean_int1', 'dbSD_int1', 'dbN_int1', 'ubssSum_int1', 'ubssMean_int1', 'ubsdSum_int1', 'ubsdMean_int1', 'utssmoss_int1', 'utsmmosm_int1', 'utssdoss_int1', 'utsmdosm_int1', 'utssmods_int1', 'utsmmodm_int1', 'utssdods_int1', 'utsmdodm_int1', 'Unnamed: 48_int1', 'idx_int2', 'x_int2', 'y_int2', 'z_int2', 'sLen2d_int2', 'sLen3d_int2', 'intmSeconds_int2', 'isDirty_int2', 'intBad_int2', 'intManual_int2', 'spineWidth_int2', 'extendHead_int2', 'extendTail_int2', 'scaleRadius_int2', 'zPlusMinus_int2', 'sSum_int2', 'sMean_int2', 'sSD_int2', 'sN_int2', 'sbSum_int2', 'sbMean_int2', 'sbSD_int2', 'sbN_int2', 'sbxyManual_int2', 'sbxPos_int2', 'sbyPos_int2', 'dSum_int2', 'dMean_int2', 'dSD_int2', 'dN_int2', 'dPlus_int2', 'dMinus_int2', 'dbSum_int2', 'dbMean_int2', 'dbSD_int2', 'dbN_int2', 'ubssSum_int2', 'ubssMean_int2', 'ubsdSum_int2', 'ubsdMean_int2', 'utssmoss_int2', 'utsmmosm_int2', 'utssdoss_int2', 'utsmdosm_int2', 'utssmods_int2', 'utsmmodm_int2', 'utssdods_int2', 'utsmdodm_int2', 'Unnamed: 48_int2']\n"
"['Idx', 'roiType', 'roiTypeNum', 'x', 'y', 'z', 'channel', 'groupID', 'parentID', 'cPnt', 'sDist', 'pDist', 'cAuto', 'cAngle', 'cLine', 'cLineNum', 'cx', 'cy', 'cz', 'cDate', 'cTime', 'mDate', 'mTime', 'cSeconds', 'mSeconds', 'userName', 'note', 'edgeList', 'isDirty', 'isBad', 'dynBad', 'intBad', 'progType', 'madeFrom', 'analParam', 'analResult1', 'analResult2', 'analResult3', 'analResult4', 'user1', 'user2', 'user3', 'userBool1', 'userBool2', 'userBool3', 'userType', 'bSpineMap', 'bSpineIdx', 'error', 'warning', 'mapName', 'mapSession', 'next', 'nexttp', 'prev', 'prevtp', 'runIdx', 'days', 'sessCond', 'mapCond', 'isAdd', 'isSub', 'isTransient', 'idx_int1', 'x_int1', 'y_int1', 'z_int1', 'sLen2d_int1', 'sLen3d_int1', 'intmSeconds_int1', 'isDirty_int1', 'intBad_int1', 'intManual_int1', 'spineWidth_int1', 'extendHead_int1', 'extendTail_int1', 'scaleRadius_int1', 'zPlusMinus_int1', 'sSum_int1', 'sMean_int1', 'sSD_int1', 'sN_int1', 'sbSum_int1', 'sbMean_int1', 'sbSD_int1', 'sbN_int1', 'sbxyManual_int1', 'sbxPos_int1', 'sbyPos_int1', 'dSum_int1', 'dMean_int1', 'dSD_int1', 'dN_int1', 'dPlus_int1', 'dMinus_int1', 'dbSum_int1', 'dbMean_int1', 'dbSD_int1', 'dbN_int1', 'ubssSum_int1', 'ubssMean_int1', 'ubsdSum_int1', 'ubsdMean_int1', 'utssmoss_int1', 'utsmmosm_int1', 'utssdoss_int1', 'utsmdosm_int1', 'utssmods_int1', 'utsmmodm_int1', 'utssdods_int1', 'utsmdodm_int1', 'utssdtds_int1', 'utsmdtdm_int1', 'utdsdods_int1', 'utdmdodm_int1', 'uSEV_int1', 'idx_int2', 'x_int2', 'y_int2', 'z_int2', 'sLen2d_int2', 'sLen3d_int2', 'intmSeconds_int2', 'isDirty_int2', 'intBad_int2', 'intManual_int2', 'spineWidth_int2', 'extendHead_int2', 'extendTail_int2', 'scaleRadius_int2', 'zPlusMinus_int2', 'sSum_int2', 'sMean_int2', 'sSD_int2', 'sN_int2', 'sbSum_int2', 'sbMean_int2', 'sbSD_int2', 'sbN_int2', 'sbxyManual_int2', 'sbxPos_int2', 'sbyPos_int2', 'dSum_int2', 'dMean_int2', 'dSD_int2', 'dN_int2', 'dPlus_int2', 'dMinus_int2', 'dbSum_int2', 'dbMean_int2', 'dbSD_int2', 'dbN_int2', 'ubssSum_int2', 'ubssMean_int2', 'ubsdSum_int2', 'ubsdMean_int2', 'utssmoss_int2', 'utsmmosm_int2', 'utssdoss_int2', 'utsmdosm_int2', 'utssmods_int2', 'utsmmodm_int2', 'utssdods_int2', 'utsmdodm_int2', 'utssdtds_int2', 'utsmdtdm_int2', 'utdsdods_int2', 'utdmdodm_int2', 'uSEV_int2']\n"
]
}
],
Expand All @@ -179,7 +183,7 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 4,
"metadata": {},
"outputs": [
{
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16 changes: 7 additions & 9 deletions examples/e - mmMapPlot.ipynb
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31 changes: 19 additions & 12 deletions examples/f - pooling maps.ipynb
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Expand Up @@ -16,20 +16,25 @@
"name": "stdout",
"output_type": "stream",
"text": [
"mmMapPool() loading map: BD_NGDG450\n",
"did not find segment map file, should be ok\n",
"map BD_NGDG450 loaded in 0.72 seconds.\n",
"mmMapPool() loading map: rr30a\n",
"map rr30a loaded in 0.45 seconds.\n",
"map rr30a loaded in 0.46 seconds.\n",
"mmMapPool() loading map: rr49c\n",
"map rr49c loaded in 0.31 seconds.\n",
"map rr49c loaded in 0.34 seconds.\n",
"mmMapPool() loading map: rr50b\n",
"map rr50b loaded in 0.47 seconds.\n",
"map rr50b loaded in 0.49 seconds.\n",
"mmMapPool() loading map: rr52c\n",
"map rr52c loaded in 0.55 seconds.\n",
"map rr52c loaded in 0.59 seconds.\n",
"mmMapPool() loading map: rr58b\n",
"map rr58b loaded in 0.7 seconds.\n",
"map rr58b loaded in 0.75 seconds.\n",
"mmMapPool() loading map: rr58c\n",
"map rr58c loaded in 0.39 seconds.\n",
"mmMapPool() loaded 6 maps in 2.86541891098 seconds.\n",
"pool: num maps:6 num obj:13705\n"
"map rr58c loaded in 0.42 seconds.\n",
"mmMapPool() loading map: THet2a\n",
"map THet2a loaded in 0.52 seconds.\n",
"mmMapPool() loaded 8 maps in 4.29251289368 seconds.\n",
"pool: num maps:8 num obj:18426\n"
]
}
],
Expand Down Expand Up @@ -59,12 +64,14 @@
"name": "stdout",
"output_type": "stream",
"text": [
"map:BD_NGDG450 map segments:0 stacks:23 total object:2664\n",
"map:rr30a map segments:5 stacks:9 total object:2467\n",
"map:rr49c map segments:3 stacks:6 total object:1343\n",
"map:rr50b map segments:4 stacks:10 total object:2173\n",
"map:rr52c map segments:3 stacks:13 total object:1972\n",
"map:rr58b map segments:3 stacks:15 total object:4246\n",
"map:rr58c map segments:3 stacks:10 total object:1504\n"
"map:rr58c map segments:3 stacks:10 total object:1504\n",
"map:THet2a map segments:4 stacks:14 total object:2057\n"
]
}
],
Expand All @@ -82,14 +89,14 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"map pool has 6 maps and 63 stacks.\n"
"map pool has 8 maps and 100 stacks.\n"
]
}
],
Expand Down Expand Up @@ -122,7 +129,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"mmStackPool() loaded 0 stacks in 0.000385046005249 seconds.\n",
"mmStackPool() loaded 0 stacks in 0.000380039215088 seconds.\n",
"pool: num stacks:0 num obj:0\n"
]
}
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4 changes: 3 additions & 1 deletion notes.md
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Expand Up @@ -11,7 +11,9 @@ mmserver.py needs this BEFORE importing any matplotlib
import matplotlib
matplotlib.use('TkAgg')

2) write out and test full virtual env install, missing flask for example !!!
2) need to remove plot import from __init__.py

3) write out and test full virtual env install, missing flask for example !!!

### Using fresh install of Anaconda on OSX

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2 changes: 1 addition & 1 deletion pymapmanager/__init__.py
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Expand Up @@ -12,7 +12,7 @@
from .mmMap import mmMap
from .mmStack import mmStack
from .mmStack import mmio
from .mmMapPlot2 import mmMapPlot2
#from .mmMapPlot2 import mmMapPlot2

"""
This will allow pymapmanager package to have a __version__ string
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4 changes: 2 additions & 2 deletions pymapmanager/mmMapPlot2.py
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Expand Up @@ -19,8 +19,8 @@
"""
from __future__ import print_function

import matplotlib
matplotlib.use('TkAgg')
#import matplotlib
#matplotlib.use('TkAgg')

import matplotlib.pyplot as plt
import numpy as np
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