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Merged
chris-allan merged 2 commits into from
Jul 18, 2013
Merged

Zooming figures export #34

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2f9837c
Image.resize ANTIALIAS in ROI_Split_Figure. See #11267
Jul 12, 2013
314b090
Batch_Image_Export 'Zoom' param. See #11268
Jul 12, 2013
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48 changes: 27 additions & 21 deletions omero/export_scripts/Batch_Image_Export.py
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Original file line number Diff line number Diff line change
Expand Up @@ -45,6 +45,11 @@
import zipfile
from datetime import datetime

try:
from PIL import Image # see ticket:2597
except ImportError:
import Image

# keep track of log strings.
logStrings = []

Expand All @@ -71,7 +76,7 @@ def compress(target, base):
finally:
zip_file.close()

def savePlane(image, format, cName, zRange, projectZ, t=0, channel=None, greyscale=False, imgWidth=None, folder_name=None):
def savePlane(image, format, cName, zRange, projectZ, t=0, channel=None, greyscale=False, zoomPercent=None, folder_name=None):
"""
Renders and saves an image to disk.

Expand All @@ -81,7 +86,7 @@ def savePlane(image, format, cName, zRange, projectZ, t=0, channel=None, greysca
@param t: T index
@param channel: Active channel index. If None, use current rendering settings
@param greyscale: If true, all visible channels will be greyscale
@param imgWidth: Resize image to this width if specified.
@param zoomPercent: Resize image by this percent if specified.
"""

originalName = image.getName()
Expand All @@ -94,7 +99,7 @@ def savePlane(image, format, cName, zRange, projectZ, t=0, channel=None, greysca
log("t: %s" % t)
#log("channel %s" % channel)
#log("greyscale %s" % greyscale)
#log("imgWidth %s" % imgWidth)
#log("zoomPercent %s" % zoomPercent)

# if channel == None: use current rendering settings
if channel != None:
Expand All @@ -108,10 +113,10 @@ def savePlane(image, format, cName, zRange, projectZ, t=0, channel=None, greysca

# All Z and T indices in this script are 1-based, but this method uses 0-based.
plane = image.renderImage(zRange[0]-1, t-1)
if imgWidth:
if zoomPercent:
w, h = plane.size
newH = (float(imgWidth) / w ) * h
plane = plane.resize((imgWidth, int(newH)))
fraction = (float(zoomPercent) / 100 )
plane = plane.resize((w * fraction, h * fraction), Image.ANTIALIAS)

if format == "PNG":
imgName = makeImageName(originalName, cName, zRange, t, "png", folder_name)
Expand Down Expand Up @@ -177,7 +182,7 @@ def saveAsOmeTiff(conn, image, folder_name=None):


def savePlanesForImage(conn, image, sizeC, splitCs, mergedCs, channelNames=None,
zRange=None, tRange=None, greyscale=False, imgWidth=None, projectZ=False, format="PNG", folder_name=None):
zRange=None, tRange=None, greyscale=False, zoomPercent=None, projectZ=False, format="PNG", folder_name=None):
"""
Saves all the required planes for a single image, either as individual planes or projection.

Expand All @@ -187,7 +192,7 @@ def savePlanesForImage(conn, image, sizeC, splitCs, mergedCs, channelNames=None,
@param zRange: Tuple: (zStart, zStop). If None, use default Zindex
@param tRange: Tuple: (tStart, tStop). If None, use default Tindex
@param greyscale: If true, all visible channels will be greyscale
@param imgWidth: Resize image to this width if specified.
@param zoomPercent: Resize image by this percent if specified.
@param projectZ: If true, project over Z range.
"""

Expand Down Expand Up @@ -230,15 +235,15 @@ def savePlanesForImage(conn, image, sizeC, splitCs, mergedCs, channelNames=None,
for t in tIndexes:
if zRange == None:
defaultZ = image.getDefaultZ()+1
savePlane(image, format, cName, (defaultZ,), projectZ, t, c, gScale, imgWidth, folder_name)
savePlane(image, format, cName, (defaultZ,), projectZ, t, c, gScale, zoomPercent, folder_name)
elif projectZ:
savePlane(image, format, cName, zRange, projectZ, t, c, gScale, imgWidth, folder_name)
savePlane(image, format, cName, zRange, projectZ, t, c, gScale, zoomPercent, folder_name)
else:
if len(zRange) > 1:
for z in range(zRange[0], zRange[1]):
savePlane(image, format, cName, (z,), projectZ, t, c, gScale, imgWidth, folder_name)
savePlane(image, format, cName, (z,), projectZ, t, c, gScale, zoomPercent, folder_name)
else:
savePlane(image, format, cName, zRange, projectZ, t, c, gScale, imgWidth, folder_name)
savePlane(image, format, cName, zRange, projectZ, t, c, gScale, zoomPercent, folder_name)


def batchImageExport(conn, scriptParams):
Expand All @@ -261,9 +266,9 @@ def batchImageExport(conn, scriptParams):
channelNames = []
if "Channel_Names" in scriptParams:
channelNames = scriptParams["Channel_Names"]
imgWidth = None
if "Image_Width" in scriptParams:
imgWidth = scriptParams["Image_Width"]
zoomPercent = None
if "Zoom" in scriptParams and scriptParams["Zoom"] != "100%":
zoomPercent = int(scriptParams["Zoom"][:-1])


# functions used below for each imaage.
Expand Down Expand Up @@ -373,15 +378,15 @@ def getTrange(sizeT, scriptParams):
elif len(tRange) == 1: log(" T-index: %d" % tRange[0])
else: log(" T-range: %s-%s" % ( tRange[0],tRange[1]-1) )
log(" Format: %s" % format)
if imgWidth is None: log(" Image Width: no resize")
else: log(" Image Width: %s" % imgWidth)
if zoomPercent is None: log(" Image Zoom: 100%")
else: log(" Image Zoom: %s" % zoomPercent)
log(" Greyscale: %s" % greyscale)
log("Channel Rendering Settings:")
for ch in img.getChannels():
log(" %s: %d-%d" % (ch.getLabel(), ch.getWindowStart(), ch.getWindowEnd()) )

savePlanesForImage(conn, img, sizeC, splitCs, mergedCs, channelNames,
zRange, tRange, greyscale, imgWidth, projectZ=projectZ, format=format, folder_name=folder_name)
zRange, tRange, greyscale, zoomPercent, projectZ=projectZ, format=format, folder_name=folder_name)

# write log for exported images (not needed for ome-tiff)
logFile = open(os.path.join(exp_dir, 'Batch_Image_Export.txt'), 'w')
Expand Down Expand Up @@ -434,6 +439,7 @@ def runScript():
tChoices = [rstring(defaultToption),
rstring('ALL T planes'),
rstring('Other (see below)')]
zoomPercents = omero.rtypes.wrap(["25%", "50%", "100%", "200%", "300%", "400%"])

client = scripts.client('Batch_Image_Export.py', """Save multiple images as jpegs or pngs in a zip
file available for download as a batch export.
Expand Down Expand Up @@ -480,9 +486,9 @@ def runScript():

scripts.Int("...specify_T_end", grouping="6.3",
description="Choose a specific T-index to export", min=1),
scripts.Int("Image_Width", grouping="7",
description="The max width of each image panel. Default is actual size", min=1),

scripts.String("Zoom", grouping="7", values=zoomPercents,
description="Zoom (jpeg, png or tiff) before saving with ANTIALIAS interpolation", default="100%"),

scripts.String("Format", grouping="8",
description="Format to save image", values=formats, default='JPEG'),
Expand Down
4 changes: 2 additions & 2 deletions omero/figure_scripts/ROI_Split_Figure.py
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Original file line number Diff line number Diff line change
Expand Up @@ -171,7 +171,7 @@ def getROIsplitView (re, pixels, zStart, zEnd, splitIndexes, channelNames, me
roiImage.load() # hoping that when we zoom, don't zoom fullImage
if roiZoom is not 1:
newSize = (int(roiWidth*roiZoom), int(roiHeight*roiZoom))
roiImage = roiImage.resize(newSize)
roiImage = roiImage.resize(newSize, Image.ANTIALIAS)
renderedImages.append(roiImage)
panelWidth = roiImage.size[0]
re.setActive(index, False) # turn the channel off again!
Expand Down Expand Up @@ -202,7 +202,7 @@ def getROIsplitView (re, pixels, zStart, zEnd, splitIndexes, channelNames, me
roiMergedImage.load() # make sure this is not just a lazy copy of the full image
if roiZoom is not 1:
newSize = (int(roiWidth*roiZoom), int(roiHeight*roiZoom))
roiMergedImage = roiMergedImage.resize(newSize)
roiMergedImage = roiMergedImage.resize(newSize, Image.ANTIALIAS)

if channelMismatch:
log(" WARNING channel mismatch: The current image has fewer channels than the primary image.")
Expand Down