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Numpy pixels type #387

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Numpy pixels type #387

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9c22335
Add pixels.get_numpy_pixels_type()
will-moore Dec 13, 2023
359c48b
OMERO_NUMPY_DTYPES holds types not strings
will-moore Dec 13, 2023
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50 changes: 27 additions & 23 deletions src/omero/gateway/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,7 @@
from past.builtins import basestring
from past.utils import old_div
from builtins import object
import numpy
import os

import warnings
Expand Down Expand Up @@ -85,6 +86,16 @@

logger = logging.getLogger(__name__)
THISPATH = os.path.dirname(os.path.abspath(__file__))
OMERO_NUMPY_DTYPES = {
PixelsTypeint8: numpy.int8,
PixelsTypeuint8: numpy.uint8,
PixelsTypeint16: numpy.int16,
PixelsTypeuint16: numpy.uint16,
PixelsTypeint32: numpy.int32,
PixelsTypeuint32: numpy.uint32,
PixelsTypefloat: numpy.float32,
PixelsTypedouble: numpy.float64,
}

try:
from PIL import Image, ImageDraw, ImageFont # see ticket:2597
Expand Down Expand Up @@ -3776,8 +3787,6 @@ def planeGen():
containerService = self.getContainerService()
updateService = self.getUpdateService()

import numpy

def createImage(firstPlane, channelList):
""" Create our new Image once we have the first plane in hand """
convertToType = None
Expand All @@ -3792,16 +3801,8 @@ def createImage(firstPlane, channelList):
# of our new image
img = self.getObject("Image", iId.getValue())
newPtype = img.getPrimaryPixels().getPixelsType().getValue()
omeroToNumpy = {PixelsTypeint8: 'int8',
PixelsTypeuint8: 'uint8',
PixelsTypeint16: 'int16',
PixelsTypeuint16: 'uint16',
PixelsTypeint32: 'int32',
PixelsTypeuint32: 'uint32',
PixelsTypefloat: 'float32',
PixelsTypedouble: 'double'}
if omeroToNumpy[newPtype] != firstPlane.dtype.name:
convertToType = getattr(numpy, omeroToNumpy[newPtype])
if OMERO_NUMPY_DTYPES[newPtype] != firstPlane.dtype.name:
convertToType = OMERO_NUMPY_DTYPES[newPtype]
img._obj.setName(rstring(imageName))
img._obj.setSeries(rint(0))
updateService.saveObject(img._obj, self.SERVICE_OPTS)
Expand Down Expand Up @@ -7495,6 +7496,10 @@ def getPlane(self, theZ=0, theC=0, theT=0):
planeList = list(self.getPlanes([(theZ, theC, theT)]))
return planeList[0]

def get_numpy_pixels_type(self):
pixels_type = self.getPixelsType().value
return OMERO_NUMPY_DTYPES[pixels_type]

def getTiles(self, zctTileList):
"""
Returns generator of numpy 2D planes from this set of pixels for a
Expand All @@ -7504,22 +7509,21 @@ def getTiles(self, zctTileList):
:param zctrList: A list of indexes: [(z,c,t, region), ]
"""

import numpy
from struct import unpack

pixelTypes = {PixelsTypeint8: ['b', numpy.int8],
PixelsTypeuint8: ['B', numpy.uint8],
PixelsTypeint16: ['h', numpy.int16],
PixelsTypeuint16: ['H', numpy.uint16],
PixelsTypeint32: ['i', numpy.int32],
PixelsTypeuint32: ['I', numpy.uint32],
PixelsTypefloat: ['f', numpy.float32],
PixelsTypedouble: ['d', numpy.float64]}
pixelTypes = {PixelsTypeint8: 'b',
PixelsTypeuint8: 'B',
PixelsTypeint16: 'h',
PixelsTypeuint16: 'H',
PixelsTypeint32: 'i',
PixelsTypeuint32: 'I',
PixelsTypefloat: 'f',
PixelsTypedouble: 'd'}
rawPixelsStore = None
sizeX = self.sizeX
sizeY = self.sizeY
pixelType = self.getPixelsType().value
numpyType = pixelTypes[pixelType][1]
numpyType = self.get_numpy_pixels_type()
exc = None
try:
rawPixelsStore = self._prepareRawPixelsStore()
Expand All @@ -7537,7 +7541,7 @@ def getTiles(self, zctTileList):
planeX = width
# +str(sizeX*sizeY)+pythonTypes[pixelType]
convertType = '>%d%s' % (
(planeY*planeX), pixelTypes[pixelType][0])
(planeY*planeX), pixelTypes[pixelType])
if isinstance(rawPlane, bytes):
convertedPlane = unpack(convertType, rawPlane)
else:
Expand Down