logging.basicConfig(level=logging.DEBUG)
# Handles args to MacOS "Apps"
if len(sys.argv) > 1 and sys.argv[1].startswith('-psn'):
del sys.argv[1]
if len(sys.argv) > 1:
# Load a properties file if passed in args
p = Properties()
if sys.argv[1] == '--incell':
# GE Incell xml wrapper
# LOOP
p.LoadIncellFiles(sys.argv[2], sys.argv[3], sys.argv[4:])
else:
p.LoadFile(sys.argv[1])
from cpa.cpatool import CPATool
import inspect
import cpa.multiclasssql
# ---
import wx
ID_CLASSIFIER = wx.NewIdRef()
ID_IMAGE_GALLERY = wx.NewIdRef()
ID_PLATE_VIEWER = wx.NewIdRef()
ID_TABLE_VIEWER = wx.NewIdRef()
ID_IMAGE_VIEWER = wx.NewIdRef()
ID_SCATTER = wx.NewIdRef()
ID_HISTOGRAM = wx.NewIdRef()
from io import StringIO
import cpa.fastgentleboostingmulticlass
import cpa.imagetools
import cpa.multiclasssql
import cpa.polyafit
import numpy
import os
import wx
from cpa.classifier import *
import time
if __name__ == "__main__":
app = wx.PySimpleApp()
p = Properties()
db = dbconnect.DBConnect()
dm = DataModel()
# props = '/Volumes/imaging_analysis/2007_10_19_Gilliland_LeukemiaScreens/Screen3_1Apr09_run3/2007_10_19_Gilliland_LeukemiaScreens_Validation_v2_AllBatches_DuplicatesFiltered_FullBarcode_testSinglePlate.properties'
# ts = '/Volumes/imaging_analysis/2007_10_19_Gilliland_LeukemiaScreens/Screen3_1Apr09_run3/trainingvalidation3b.txt'
props = '../Properties/nirht_area_test.properties'
ts = '/Users/afraser/Desktop/MyTrainingSet.txt'
p.LoadFile(props)
classifier = Classifier(p)
classifier.Show(True)
classifier.LoadTrainingSet(ts)
time.sleep(3)
classifier.TrainClassifier()
classifier.ScoreAll()
app.MainLoop()
class TestDBConnect(unittest.TestCase):
def setup_mysql(self):
self.p = Properties()
self.db = DBConnect()
self.db.Disconnect()
self.p.LoadFile('../../CPAnalyst_test_data/nirht_test.properties')
def setup_sqlite(self):
self.p = Properties()
self.db = DBConnect()
self.db.Disconnect()
self.p.LoadFile('../../CPAnalyst_test_data/nirht_local.properties')
def setup_sqlite2(self):
self.p = Properties()
self.db = DBConnect()
self.db.Disconnect()
self.p.LoadFile(
'../../CPAnalyst_test_data/export_to_db_test.properties')
#
# Test module-level functions
#
def test_clean_up_colnames(self):
self.setup_mysql()
def test_well_key_columns(self):
self.setup_mysql()
assert well_key_columns() == ('plate', 'well')
self.setup_sqlite()
assert well_key_columns() == tuple()
def test_image_key_columns(self):
self.setup_mysql()
assert image_key_columns() == ('ImageNumber', )
self.setup_sqlite()
assert image_key_columns() == ('TableNumber', 'ImageNumber')
def test_object_key_columns(self):
self.setup_mysql()
assert object_key_columns() == ('ImageNumber', 'ObjectNumber')
self.setup_sqlite()
assert object_key_columns() == ('TableNumber', 'ImageNumber',
'ObjectNumber')
def test_GetWhereClauseForObjects(self):
self.setup_mysql()
assert GetWhereClauseForObjects([
(1, 1)
]) == '(ImageNumber=1 AND ObjectNumber=1)'
assert GetWhereClauseForObjects(
[(1, 1), (2, 1)]
) == '(ImageNumber=1 AND ObjectNumber=1 OR ImageNumber=2 AND ObjectNumber=1)'
self.setup_sqlite()
assert GetWhereClauseForObjects(
[(0, 1, 1), (0, 2, 1)]
) == '(TableNumber=0 AND ImageNumber=1 AND ObjectNumber=1 OR TableNumber=0 AND ImageNumber=2 AND ObjectNumber=1)'
def test_GetWhereClauseForImages(self):
self.setup_mysql()
assert GetWhereClauseForImages([(1, )]) == 'ImageNumber IN (1)'
assert GetWhereClauseForImages([(1, ),
(2, )]) == 'ImageNumber IN (1,2)'
self.setup_sqlite()
assert GetWhereClauseForImages([
(0, 1), (0, 2)
]) == '(TableNumber=0 AND ImageNumber IN (1,2))'
def test_UniqueObjectClause(self):
self.setup_mysql()
assert UniqueObjectClause() == 'ImageNumber,ObjectNumber'
self.setup_sqlite()
assert UniqueObjectClause() == 'TableNumber,ImageNumber,ObjectNumber'
def test_UniqueImageClause(self):
self.setup_mysql()
assert UniqueImageClause() == 'ImageNumber'
self.setup_sqlite()
assert UniqueImageClause() == 'TableNumber,ImageNumber'
#
# Test class functions
#
def test_Connect_Disconnect(self):
self.setup_mysql()
self.db.connect()
assert len(self.db.connections) == 1
assert len(self.db.cursors) == 1
assert len(self.db.connectionInfo) == 1
self.db.connect()
assert len(self.db.connections) == 1
assert len(self.db.cursors) == 1
assert len(self.db.connectionInfo) == 1
self.db.Disconnect()
assert len(self.db.connections) == 0
assert len(self.db.cursors) == 0
assert len(self.db.connectionInfo) == 0
self.setup_sqlite()
assert len(self.db.connections) == 0
assert len(self.db.cursors) == 0
assert len(self.db.connectionInfo) == 0
self.db.GetAllImageKeys()
assert len(self.db.connections) == 1
assert len(self.db.cursors) == 1
assert len(self.db.connectionInfo) == 1
self.db.GetAllImageKeys()
assert len(self.db.connections) == 1
assert len(self.db.cursors) == 1
assert len(self.db.connectionInfo) == 1
self.db.Disconnect()
assert len(self.db.connections) == 0
assert len(self.db.cursors) == 0
assert len(self.db.connectionInfo) == 0
def test_Commit(self):
self.setup_mysql()
self.db.connect()
self.db.execute('DROP TABLE IF EXISTS temp_test')
self.db.execute('CREATE TABLE temp_test (id int(11) default NULL)')
self.db.execute('INSERT INTO temp_test values(1)')
self.db.Commit()
self.db.Disconnect()
self.db.connect()
res = self.db.execute('SELECT id FROM temp_test WHERE id=1')
assert res == [(1, )]
self.db.execute('DROP TABLE temp_test')
def test_execute(self):
self.setup_mysql()
self.db.execute('SELECT %s FROM %s' %
(self.p.image_id, self.p.image_table))
self.setup_sqlite()
self.db.execute('SELECT %s FROM %s' %
(self.p.image_id, self.p.image_table))
def test_GetObjectIDAtIndex(self):
self.setup_mysql()
obKey = self.db.GetObjectIDAtIndex(imKey=(1, ), index=94)
assert obKey == (1, 94)
self.setup_sqlite()
obKey = self.db.GetObjectIDAtIndex(imKey=(0, 1), index=94)
assert obKey == (0, 1, 94)
def test_GetPerImageObjectCounts(self):
self.setup_mysql()
self.db.GetPerImageObjectCounts()
self.setup_sqlite()
self.db.GetPerImageObjectCounts()
def test_GetObjectCoords(self):
self.setup_mysql()
xy = self.db.GetObjectCoords((1, 1))
assert xy == (11.4818, 305.06400000000002)
self.setup_sqlite()
xy = self.db.GetObjectCoords((0, 1, 1))
assert xy == (11.4818, 305.06400000000002)
def test_GetObjectNear(self):
self.setup_mysql()
obKey = self.db.GetObjectNear((1, ), 11, 300)
assert obKey == (1, 1)
self.setup_sqlite()
obKey = self.db.GetObjectNear((0, 1), 11, 300)
assert obKey == (0, 1, 1)
def test_GetFullChannelPathsForImage(self):
self.setup_mysql()
paths = self.db.GetFullChannelPathsForImage((1, ))
assert paths == [
'2006_02_15_NIRHT/trcHT29Images/NIRHTa+001/AS_09125_050116000001_A01f00d2.DIB',
'2006_02_15_NIRHT/trcHT29Images/NIRHTa+001/AS_09125_050116000001_A01f00d1.DIB',
'2006_02_15_NIRHT/trcHT29Images/NIRHTa+001/AS_09125_050116000001_A01f00d0.DIB'
]
self.setup_sqlite()
paths = self.db.GetFullChannelPathsForImage((0, 1))
assert paths == [
'2006_02_15_NIRHT/trcHT29Images/NIRHTa+001/AS_09125_050116000001_A01f00d2.DIB',
'2006_02_15_NIRHT/trcHT29Images/NIRHTa+001/AS_09125_050116000001_A01f00d1.DIB',
'2006_02_15_NIRHT/trcHT29Images/NIRHTa+001/AS_09125_050116000001_A01f00d0.DIB'
]
def test_GetGroupMaps(self):
self.setup_mysql()
groupMaps, colNames = self.db.GetGroupMaps()
assert groupMaps['Gene'][(1, )] == ('Gabra3', )
assert groupMaps['Well'][(1, )] == (1, )
assert groupMaps['Well+Gene'][(1, )] == (1, 'Gabra3')
assert colNames == {
'Gene': ['gene'],
'Well': ['well'],
'Well+Gene': ['well', 'gene']
}
self.setup_sqlite()
groupMaps, colNames = self.db.GetGroupMaps()
assert groupMaps['96x4'][(0, 1)] == (0, 1)
assert colNames == {'96x4': ['T2', 'I2']}
def test_GetFilteredImages(self):
self.setup_mysql()
test = set(self.db.GetFilteredImages('MAPs'))
print(test)
vals = set([(239, ), (21, ), (32, ), (197, ), (86, ), (23, ), (61, ),
(72, ), (213, ), (222, ), (63, ), (229, ), (221, ), (38, ),
(224, ), (231, ), (13, ), (24, ), (78, ), (214, ), (15, ),
(223, ), (53, ), (64, ), (246, ), (55, ), (93, ), (232, ),
(30, ), (206, ), (95, ), (215, ), (5, ), (16, ), (70, ),
(7, ), (45, ), (56, ), (238, ), (198, ), (47, ), (207, ),
(85, ), (96, ), (22, ), (87, ), (253, ), (8, ), (62, ),
(254, ), (255, ), (199, ), (37, ), (48, ), (205, ),
(230, ), (208, ), (39, ), (77, ), (88, ), (14, ), (79, ),
(245, ), (256, ), (54, ), (247, ), (29, ), (40, ), (94, ),
(31, ), (240, ), (69, ), (80, ), (6, ), (216, ), (71, ),
(237, ), (248, ), (200, ), (46, )])
assert test == vals
assert self.db.GetFilteredImages('IMPOSSIBLE') == []
self.setup_sqlite()
assert self.db.GetFilteredImages('FirstTen') == [
(0, 1), (0, 2), (0, 3), (0, 4), (0, 5), (0, 6), (0, 7), (0, 8),
(0, 9), (0, 10)
]
assert self.db.GetFilteredImages('IMPOSSIBLE') == []
def test_GetColumnNames(self):
self.setup_mysql()
cols = self.db.GetColumnNames(self.p.object_table)
assert cols[:19] == [
'ImageNumber', 'ObjectNumber', 'Nuclei_Location_CenterX',
'Nuclei_Location_CenterY', 'Nuclei_Children_Cells_Count',
'Nuclei_Correlation_Correlation_DNA_and_pH3',
'Nuclei_Correlation_Correlation_DNA_and_Actin',
'Nuclei_Correlation_Correlation_pH3_and_Actin',
'Nuclei_AreaShape_Area', 'Nuclei_AreaShape_Eccentricity',
'Nuclei_AreaShape_Solidity', 'Nuclei_AreaShape_Extent',
'Nuclei_AreaShape_Euler_number', 'Nuclei_AreaShape_Perimeter',
'Nuclei_AreaShape_Form_factor', 'Nuclei_AreaShape_MajorAxisLength',
'Nuclei_AreaShape_MinorAxisLength', 'Nuclei_AreaShape_Orientation',
'Nuclei_AreaShape_Zernike0_0'
]
assert cols[-20:] == [
'AreaNormalized_Cytoplasm_AreaShape_Zernike5_3',
'AreaNormalized_Cytoplasm_AreaShape_Zernike5_5',
'AreaNormalized_Cytoplasm_AreaShape_Zernike6_0',
'AreaNormalized_Cytoplasm_AreaShape_Zernike6_2',
'AreaNormalized_Cytoplasm_AreaShape_Zernike6_4',
'AreaNormalized_Cytoplasm_AreaShape_Zernike6_6',
'AreaNormalized_Cytoplasm_AreaShape_Zernike7_1',
'AreaNormalized_Cytoplasm_AreaShape_Zernike7_3',
'AreaNormalized_Cytoplasm_AreaShape_Zernike7_5',
'AreaNormalized_Cytoplasm_AreaShape_Zernike7_7',
'AreaNormalized_Cytoplasm_AreaShape_Zernike8_0',
'AreaNormalized_Cytoplasm_AreaShape_Zernike8_2',
'AreaNormalized_Cytoplasm_AreaShape_Zernike8_4',
'AreaNormalized_Cytoplasm_AreaShape_Zernike8_6',
'AreaNormalized_Cytoplasm_AreaShape_Zernike8_8',
'AreaNormalized_Cytoplasm_AreaShape_Zernike9_1',
'AreaNormalized_Cytoplasm_AreaShape_Zernike9_3',
'AreaNormalized_Cytoplasm_AreaShape_Zernike9_5',
'AreaNormalized_Cytoplasm_AreaShape_Zernike9_7',
'AreaNormalized_Cytoplasm_AreaShape_Zernike9_9'
]
self.setup_sqlite()
cols = self.db.GetColumnNames(self.p.object_table)
assert cols[:20] == [
'TableNumber', 'ImageNumber', 'ObjectNumber',
'Nuclei_Location_CenterX', 'Nuclei_Location_CenterY',
'Nuclei_Children_Cells_Count',
'Nuclei_Correlation_Correlation_DNA_and_pH3',
'Nuclei_Correlation_Correlation_DNA_and_Actin',
'Nuclei_Correlation_Correlation_pH3_and_Actin',
'Nuclei_AreaShape_Area', 'Nuclei_AreaShape_Eccentricity',
'Nuclei_AreaShape_Solidity', 'Nuclei_AreaShape_Extent',
'Nuclei_AreaShape_Euler_number', 'Nuclei_AreaShape_Perimeter',
'Nuclei_AreaShape_Form_factor', 'Nuclei_AreaShape_MajorAxisLength',
'Nuclei_AreaShape_MinorAxisLength', 'Nuclei_AreaShape_Orientation',
'Nuclei_AreaShape_Zernike0_0'
]
assert cols[-20:] == [
'AreaNormalized_Cytoplasm_AreaShape_Zernike5_3',
'AreaNormalized_Cytoplasm_AreaShape_Zernike5_5',
'AreaNormalized_Cytoplasm_AreaShape_Zernike6_0',
'AreaNormalized_Cytoplasm_AreaShape_Zernike6_2',
'AreaNormalized_Cytoplasm_AreaShape_Zernike6_4',
'AreaNormalized_Cytoplasm_AreaShape_Zernike6_6',
'AreaNormalized_Cytoplasm_AreaShape_Zernike7_1',
'AreaNormalized_Cytoplasm_AreaShape_Zernike7_3',
'AreaNormalized_Cytoplasm_AreaShape_Zernike7_5',
'AreaNormalized_Cytoplasm_AreaShape_Zernike7_7',
'AreaNormalized_Cytoplasm_AreaShape_Zernike8_0',
'AreaNormalized_Cytoplasm_AreaShape_Zernike8_2',
'AreaNormalized_Cytoplasm_AreaShape_Zernike8_4',
'AreaNormalized_Cytoplasm_AreaShape_Zernike8_6',
'AreaNormalized_Cytoplasm_AreaShape_Zernike8_8',
'AreaNormalized_Cytoplasm_AreaShape_Zernike9_1',
'AreaNormalized_Cytoplasm_AreaShape_Zernike9_3',
'AreaNormalized_Cytoplasm_AreaShape_Zernike9_5',
'AreaNormalized_Cytoplasm_AreaShape_Zernike9_7',
'AreaNormalized_Cytoplasm_AreaShape_Zernike9_9'
]
def test_GetColumnTypes(self):
self.setup_mysql()
cols = self.db.GetColumnTypes(self.p.object_table)
assert cols[:19] == [
int, int, float, float, float, float, float, float, float, float,
float, float, float, float, float, float, float, float, float
]
assert cols[-20:] == [
float, float, float, float, float, float, float, float, float,
float, float, float, float, float, float, float, float, float,
float, float
]
cols = self.db.GetColumnTypes(self.p.image_table)
assert cols[:20] == [
int, int, int, str, int, str, str, str, str, str, str, float,
float, float, float, float, float, float, float, float
]
def test_GetColnamesForClassifier(self):
self.setup_mysql()
cols = self.db.GetColnamesForClassifier()
for c in [
'ImageNumber', 'ObjectNumber', 'Nuclei_Location_CenterX',
'Nuclei_Location_CenterY'
]:
assert c not in cols
self.setup_sqlite()
cols = self.db.GetColnamesForClassifier()
for c in [
'TableNumber', 'ImageNumber', 'ObjectNumber',
'Nuclei_Location_CenterX', 'Nuclei_Location_CenterY'
]:
assert c not in cols
def test_ReadExportToDB(self):
'''Test reading data from Export to Database.'''
self.setup_sqlite2()
vals = [(1, ), (2, ), (3, ), (4, ), (5, ), (6, ), (7, ), (8, ), (9, ),
(10, ), (11, ), (12, ), (13, ), (14, ), (15, ), (16, ), (17, ),
(18, ), (19, ), (20, )]
groups = {
'Plate+Well': {
('Week1_22123', 'B05'): [(13, ), (14, ), (15, ), (16, )],
('Week1_22123', 'B02'): [(1, ), (2, ), (3, ), (4, )],
('Week1_22123', 'B04'): [(9, ), (10, ), (11, ), (12, )],
('Week1_22123', 'B06'): [(17, ), (18, ), (19, ), (20, )],
('Week1_22123', 'B03'): [(5, ), (6, ), (7, ), (8, )]
}
}, {
'Plate+Well':
['Image_Metadata_Plate_DAPI', 'Image_Metadata_Well_DAPI']
}
assert len(self.db.GetAllImageKeys()) == 20
assert self.db.GetAllImageKeys() == vals
assert self.db.GetGroupMaps(True) == groups
def test_CreateMySQLTempTableFromData(self):
self.setup_mysql()
data = [
['A01', 1, 1.],
['A02', 1, 2.],
['A03', 1, -np.inf],
['A04', 1, np.inf],
['A04', 1, np.nan],
['A04', 1, 100],
['A04', 1, 200],
]
colnames = ['well', 'plate', 'vals']
self.db.CreateTableFromData(data,
colnames,
'__test_table',
temporary=True)
res = self.db.execute('select * from __test_table')
assert res == [('A01', 1, 1.0), ('A02', 1, 2.0), ('A03', 1, None),
('A04', 1, None), ('A04', 1, None), ('A04', 1, 100.0),
('A04', 1, 200.0)]
def test_CreateSQLiteTempTableFromData(self):
self.setup_sqlite()
data = [
['A01', 1, 1.],
['A02', 1, 2.],
['A03', 1, -np.inf],
['A04', 1, np.inf],
['A04', 1, np.nan],
['A04', 1, 100],
['A04', 1, 200],
]
colnames = ['well', 'plate', 'vals']
self.db.CreateTableFromData(data,
colnames,
'__test_table',
temporary=True)
res = self.db.execute('select * from __test_table')
assert res == [('A01', 1, 1.0), ('A02', 1, 2.0), ('A03', 1, None),
('A04', 1, None), ('A04', 1, None), ('A04', 1, 100.0),
('A04', 1, 200.0)]