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added _repr_html_ method for _ImageWrapper #394

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merged 6 commits into from
Apr 24, 2024
Merged

added _repr_html_ method for _ImageWrapper #394

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1fec7e2
added `repr_html` method for `_ImageWrapper`
jo-mueller Jan 30, 2024
1e40b2a
limited floating point precision in voxel dimensions
jo-mueller Jan 31, 2024
48d4de4
Show Image, Dataset and Project in a table
will-moore Feb 1, 2024
b945fdb
Merge pull request #1 from will-moore/repr_html
jo-mueller Feb 1, 2024
da9d644
moved `repr_html` code to utils
jo-mueller Apr 12, 2024
b0a7fad
escaped non-existing pixsizes/units
jo-mueller Apr 18, 2024
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9 changes: 8 additions & 1 deletion src/omero/gateway/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,7 @@
from omero.cmd import Chgrp2, Delete2, DoAll, SkipHead, Chown2
from omero.cmd.graphs import ChildOption
from omero.api import Save
from omero.gateway.utils import ServiceOptsDict, GatewayConfig, toBoolean
from omero.gateway.utils import ServiceOptsDict, GatewayConfig, toBoolean, image_to_html
from omero.model.enums import PixelsTypeint8, PixelsTypeuint8, PixelsTypeint16
from omero.model.enums import PixelsTypeuint16, PixelsTypeint32
from omero.model.enums import PixelsTypeuint32, PixelsTypefloat
Expand Down Expand Up @@ -291,6 +291,13 @@ def __init__(self, conn=None, obj=None, cache=None, **kwargs):
self._conn.SERVICE_OPTS)
self.__prepare__(**kwargs)

def _repr_html_(self):
"""
Returns an HTML representation of the object. This is used by the
IPython notebook to display the object in a cell.
"""
return image_to_html(self)

def __eq__(self, a):
"""
Returns true if the object is of the same type and has same id and name
Expand Down
108 changes: 108 additions & 0 deletions src/omero/gateway/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -221,3 +221,111 @@ def propertiesToDict(m, prefix=None):
except:
d[items[-1]] = value
return nested_dict

def image_to_html(image):
import base64

try:
pixsizeX = '{:.3f}'.format(image.getPixelSizeX())
pixsizeY = '{:.3f}'.format(image.getPixelSizeY())
pixsizeZ = '{:.3f}'.format(image.getPixelSizeZ())
UnitX = image.getPixelSizeX().getUnit()
UnitY = image.getPixelSizeY().getUnit()
UnitZ = image.getPixelSizeZ().getUnit()
except:
pixsizeX, pixsizeY, pixsizeZ = 'na', 'na', 'na'
UnitX, UnitY, UnitZ = 'na', 'na', 'na'

html_style_header = """
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Image Details</title>
<style>
img {
min-width: 250px; /* Set the minimum width for all images */
min-height: 250px; /* Set the minimum height for all images */
}
.align-top {
vertical-align: top;
}
.text-right {
text-align: right;
}
</style>
</head>
"""

def obj_html(obj, otype):
return f"""<tr>
<td><b>{otype}</b></td>
<td class=text-right>{obj.id if obj else ""}</td>
<td class=text-right>{obj.name if obj else ""}</td>
</tr>
"""

# create a sub-table for image information
table_imageinfo = f"""
<table>
<tr><th></th><th>ID</th><th>Name</th></tr>
{obj_html(image, 'Image')}
{obj_html(image.getParent(), 'Dataset')}
{obj_html(image.getProject(), 'Project')}
</table>
"""

# get entries for thumbnail and dimensions
encoded_image = base64.b64encode(image.getThumbnail()).decode('utf-8')
dimensions = f"""(
{image.getSizeT()},
{image.getSizeC()},
{image.getSizeZ()},
{image.getSizeY()},
{image.getSizeX()})"""
physical_dims = f"""({pixsizeZ}, {pixsizeY}, {pixsizeX})""".format()
physical_units = f"""({UnitZ}, {UnitY}, {UnitX})"""

table_dimensions = f"""
<table>\n
<tr>\n
<td><b>Dimensions (TCZYX): </b></td> <td class=text-right>{dimensions}</td>\n
</tr>\n
<tr>\n
<td><b>Voxel/Pixel dimensions (ZYX): </b></td> <td class=text-right>{physical_dims}</td>\n
</tr>\n
<tr>\n
<td><b>Physical units: </b></td> <td class=text-right>{physical_units}</td>\n
</tr>\n
<tr>\n
<td><b>Channel Names: </b></td> <td class=text-right>{image.getChannelLabels()}</td>\n
</tr>\n
</table>
"""

table_assembly = f"""
<table>
<tr>
<td><div class="thumbnail">
<img src="data:image/jpeg;base64,{encoded_image}" alt="Thumbnail">
</div></td>
<td class="align-top"><h2>Image information </h2>
{table_imageinfo}
</td>
</tr>
</table>
<table>
<tr>
<td>{table_dimensions}</td>
</tr>
</table>
"""

return '\n'.join([
html_style_header,
'<body>',
table_assembly,
'</body>',
'</html>'
])