Exemplos de make_image_reader_class em Python

Exemplo n.º 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:]))

Exemplo n.º 2

Arquivo: test_formatreader.py Projeto: 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:]))

Exemplo n.º 3

Arquivo: test_formatreader.py Projeto: 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)

Exemplo n.º 4

 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)

Exemplo n.º 5

Arquivo: test_formatreader.py Projeto: 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)

Exemplo n.º 6

Arquivo: test_formatreader.py Projeto: 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)

Exemplo n.º 7

Arquivo: loadimagesnew.py Projeto: 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
import cellprofiler.preferences as preferences

Exemplo n.º 8

Arquivo: loadimagesnew.py Projeto: 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
import cellprofiler.preferences as preferences