Python make_format_tools_class 예제들

예제 #1

 def test_03_01_read_tif(self):
     path = os.path.join(example_images_directory(), 'ExampleSBSImages',
                         'Channel1-01-A-01.tif')
     ImageReader = F.make_image_reader_class()
     FormatTools = F.make_format_tools_class()
     reader = ImageReader()
     reader.setId(path)
     data = reader.openBytes(0)
     data.shape = (reader.getSizeY(), reader.getSizeX())
     #
     # Data as read by cellprofiler.modules.loadimages.load_using_PIL
     #
     expected_0_10_0_10 = np.array(
         [[0, 7, 7, 6, 5, 8, 4, 2, 1, 2], [0, 8, 8, 7, 6, 10, 4, 2, 2, 2],
          [0, 9, 9, 7, 8, 8, 2, 1, 3, 2], [0, 10, 9, 8, 10, 6, 2, 2, 3, 2],
          [0, 10, 10, 10, 9, 4, 2, 2, 2, 2],
          [0, 9, 9, 10, 8, 3, 2, 4, 2, 2], [0, 9, 9, 10, 8, 2, 2, 4, 3, 2],
          [0, 9, 8, 9, 7, 4, 2, 2, 2, 2], [0, 10, 11, 9, 9, 4, 2, 2, 2, 2],
          [0, 12, 13, 12, 9, 4, 2, 2, 2, 2]],
         dtype=np.uint8)
     expected_n10_n10 = np.array(
         [[2, 1, 1, 1, 2, 2, 1, 2, 1, 2], [1, 2, 2, 2, 2, 1, 1, 1, 2, 1],
          [1, 1, 1, 2, 1, 2, 2, 2, 2, 1], [2, 2, 2, 2, 3, 2, 2, 2, 2, 1],
          [1, 2, 2, 1, 1, 1, 1, 1, 2, 2], [2, 1, 2, 2, 2, 1, 1, 2, 2, 2],
          [2, 2, 3, 2, 2, 1, 2, 2, 2, 1], [3, 3, 1, 2, 2, 2, 2, 3, 2, 2],
          [3, 2, 2, 2, 2, 2, 2, 2, 3, 3], [5, 2, 3, 3, 2, 2, 2, 3, 2, 2]],
         dtype=np.uint8)
     self.assertTrue(np.all(expected_0_10_0_10 == data[:10, :10]))
     self.assertTrue(np.all(expected_n10_n10 == data[-10:, -10:]))

예제 #2

파일: test_formatreader.py 프로젝트: AnneCarpenter/python-bioformats

 def test_03_01_read_tif(self):
     path = os.path.join(os.path.dirname(__file__), 'Channel1-01-A-01.tif')
     ImageReader = F.make_image_reader_class()
     FormatTools = F.make_format_tools_class()
     reader = ImageReader()
     reader.setId(path)
     data = reader.openBytes(0)
     data.shape = (reader.getSizeY(), reader.getSizeX())
     #
     # Data as read by cellprofiler.modules.loadimages.load_using_PIL
     #
     expected_0_10_0_10 = np.array(
         [[ 0,  7,  7,  6,  5,  8,  4,  2,  1,  2],
          [ 0,  8,  8,  7,  6, 10,  4,  2,  2,  2],
          [ 0,  9,  9,  7,  8,  8,  2,  1,  3,  2],
          [ 0, 10,  9,  8, 10,  6,  2,  2,  3,  2],
          [ 0, 10, 10, 10,  9,  4,  2,  2,  2,  2],
          [ 0,  9,  9, 10,  8,  3,  2,  4,  2,  2],
          [ 0,  9,  9, 10,  8,  2,  2,  4,  3,  2],
          [ 0,  9,  8,  9,  7,  4,  2,  2,  2,  2],
          [ 0, 10, 11,  9,  9,  4,  2,  2,  2,  2],
          [ 0, 12, 13, 12,  9,  4,  2,  2,  2,  2]], dtype=np.uint8)
     expected_n10_n10 = np.array(
         [[2, 1, 1, 1, 2, 2, 1, 2, 1, 2],
          [1, 2, 2, 2, 2, 1, 1, 1, 2, 1],
          [1, 1, 1, 2, 1, 2, 2, 2, 2, 1],
          [2, 2, 2, 2, 3, 2, 2, 2, 2, 1],
          [1, 2, 2, 1, 1, 1, 1, 1, 2, 2],
          [2, 1, 2, 2, 2, 1, 1, 2, 2, 2],
          [2, 2, 3, 2, 2, 1, 2, 2, 2, 1],
          [3, 3, 1, 2, 2, 2, 2, 3, 2, 2],
          [3, 2, 2, 2, 2, 2, 2, 2, 3, 3],
          [5, 2, 3, 3, 2, 2, 2, 3, 2, 2]], dtype=np.uint8)
     self.assertTrue(np.all(expected_0_10_0_10 == data[:10,:10]))
     self.assertTrue(np.all(expected_n10_n10 == data[-10:,-10:]))

예제 #3

 def test_01_01_make_format_tools_class(self):
     FormatTools = F.make_format_tools_class()
     self.assertEqual(FormatTools.CAN_GROUP, 1)
     self.assertEqual(FormatTools.CANNOT_GROUP, 2)
     self.assertEqual(FormatTools.DOUBLE, 7)
     self.assertEqual(FormatTools.FLOAT, 6)
     self.assertEqual(FormatTools.INT16, 2)
     self.assertEqual(FormatTools.INT8, 0)
     self.assertEqual(FormatTools.MUST_GROUP, 0)
     self.assertEqual(FormatTools.UINT16, 3)
     self.assertEqual(FormatTools.UINT32, 5)
     self.assertEqual(FormatTools.UINT8, 1)

예제 #4

파일: test_formatreader.py 프로젝트: joshmoore/python-bioformats

 def test_01_01_make_format_tools_class(self):
     FormatTools = F.make_format_tools_class()
     self.assertEqual(FormatTools.CAN_GROUP, 1)
     self.assertEqual(FormatTools.CANNOT_GROUP, 2)
     self.assertEqual(FormatTools.DOUBLE, 7)
     self.assertEqual(FormatTools.FLOAT, 6)
     self.assertEqual(FormatTools.INT16, 2)
     self.assertEqual(FormatTools.INT8, 0)
     self.assertEqual(FormatTools.MUST_GROUP, 0)
     self.assertEqual(FormatTools.UINT16, 3)
     self.assertEqual(FormatTools.UINT32, 5)
     self.assertEqual(FormatTools.UINT8, 1)

예제 #5

파일: test_formatreader.py 프로젝트: joshmoore/python-bioformats

 def test_02_01_make_image_reader(self):
     path = os.path.join(os.path.dirname(__file__), "Channel1-01-A-01.tif")
     ImageReader = F.make_image_reader_class()
     FormatTools = F.make_format_tools_class()
     reader = ImageReader()
     reader.setId(path)
     self.assertEqual(reader.getDimensionOrder(), "XYCZT")
     metadata = J.jdictionary_to_string_dictionary(reader.getMetadata())
     self.assertEqual(int(metadata["ImageWidth"]), reader.getSizeX())
     self.assertEqual(int(metadata["ImageLength"]), reader.getSizeY())
     self.assertEqual(reader.getImageCount(), 1)
     self.assertEqual(reader.getSizeC(), 1)
     self.assertEqual(reader.getSizeT(), 1)
     self.assertEqual(reader.getSizeZ(), 1)
     self.assertEqual(reader.getPixelType(), FormatTools.UINT8)
     self.assertEqual(reader.getRGBChannelCount(), 1)

예제 #6

 def test_02_01_make_image_reader(self):
     path = os.path.join(example_images_directory(), 'ExampleSBSImages',
                         'Channel1-01-A-01.tif')
     ImageReader = F.make_image_reader_class()
     FormatTools = F.make_format_tools_class()
     reader = ImageReader()
     reader.setId(path)
     self.assertEqual(reader.getDimensionOrder(), "XYCZT")
     self.assertEqual(640, reader.getSizeX())
     self.assertEqual(640, reader.getSizeY())
     self.assertEqual(reader.getImageCount(), 1)
     self.assertEqual(reader.getSizeC(), 1)
     self.assertEqual(reader.getSizeT(), 1)
     self.assertEqual(reader.getSizeZ(), 1)
     self.assertEqual(reader.getPixelType(), FormatTools.UINT8)
     self.assertEqual(reader.getRGBChannelCount(), 1)

예제 #7

파일: test_formatreader.py 프로젝트: Noiraud/CellProfiler

 def test_02_01_make_image_reader(self):
     path = os.path.join(example_images_directory(), 'ExampleSBSImages',
                         'Channel1-01-A-01.tif')
     ImageReader = F.make_image_reader_class()
     FormatTools = F.make_format_tools_class()
     reader = ImageReader()
     reader.setId(path)
     self.assertEqual(reader.getDimensionOrder(), "XYCZT")
     self.assertEqual(640, reader.getSizeX())
     self.assertEqual(640, reader.getSizeY())
     self.assertEqual(reader.getImageCount(), 1)
     self.assertEqual(reader.getSizeC(), 1)
     self.assertEqual(reader.getSizeT(), 1)
     self.assertEqual(reader.getSizeZ(), 1)
     self.assertEqual(reader.getPixelType(), FormatTools.UINT8)
     self.assertEqual(reader.getRGBChannelCount(), 1)

예제 #8

파일: test_formatreader.py 프로젝트: pskeshu/python-bioformats

 def test_02_01_make_image_reader(self):
     path = os.path.join(os.path.dirname(__file__), 'Channel1-01-A-01.tif')
     ImageReader = F.make_image_reader_class()
     FormatTools = F.make_format_tools_class()
     reader = ImageReader()
     reader.setId(path)
     self.assertEqual(reader.getDimensionOrder(), "XYCZT")
     metadata = J.jdictionary_to_string_dictionary(reader.getMetadata())
     self.assertEqual(int(metadata["ImageWidth"]), reader.getSizeX())
     self.assertEqual(int(metadata["ImageLength"]), reader.getSizeY())
     self.assertEqual(reader.getImageCount(), 1)
     self.assertEqual(reader.getSizeC(), 1)
     self.assertEqual(reader.getSizeT(), 1)
     self.assertEqual(reader.getSizeZ(), 1)
     self.assertEqual(reader.getPixelType(), FormatTools.UINT8)
     self.assertEqual(reader.getRGBChannelCount(), 1)

예제 #9

파일: loadimagesnew.py 프로젝트: jsilter/CellProfiler

__version__="$Revision$"

import numpy as np
import cgi
import hashlib
import os
import re
import sys
import wx
import wx.html

try:
    import bioformats.formatreader as formatreader
    env = formatreader.get_env()
    FormatTools = formatreader.make_format_tools_class(env)
    ImageReader = formatreader.make_image_reader_class(env)
    ChannelSeparator = formatreader.make_reader_wrapper_class(
        env,"loci/formats/ChannelSeparator")
    has_bioformats = True
except:
    has_bioformats = False
import Image as PILImage
import TiffImagePlugin as TIFF
import cellprofiler.dib
import matplotlib.image
import scipy.io.matlab.mio

import cellprofiler.cpmodule as cpmodule
import cellprofiler.cpimage as cpimage
import cellprofiler.measurements as cpm

예제 #10

파일: loadimagesnew.py 프로젝트: robertRalston/CellProfiler

__version__ = "$Revision$"

import numpy as np
import cgi
import hashlib
import os
import re
import sys
import wx
import wx.html

try:
    import bioformats.formatreader as formatreader
    env = formatreader.get_env()
    FormatTools = formatreader.make_format_tools_class(env)
    ImageReader = formatreader.make_image_reader_class(env)
    ChannelSeparator = formatreader.make_reader_wrapper_class(
        env, "loci/formats/ChannelSeparator")
    has_bioformats = True
except:
    has_bioformats = False
import PIL.Image as PILImage
import PIL.TiffImagePlugin as TIFF
import cellprofiler.dib
import matplotlib.image
import scipy.io.matlab.mio

import cellprofiler.cpmodule as cpmodule
import cellprofiler.cpimage as cpimage
import cellprofiler.measurements as cpm