def image(request, imageId):
"""
Shows an image preview (single plane), Name, Description etc. links to datasets.
"""
conn = getConnection(request)
image = conn.getObject("Image", imageId)
scriptService = conn.getScriptService()
scripts = []
scriptNames = {
"/EMAN2/Nonlinear_Anisotropic_Diffusion.py": "IMOD: Nonlinear Anisotropic Diffusion",
"/EMAN2/Segger_Segmentation.py": "Segger: Segmentation",
"/EMAN2/Eman_Filters.py": "EMAN2: Filtering",
"/EMAN2/Ctf_Correction.py": "EMAN2: CTF Correction",
"/EMAN2/Run_Spider_Procedure.py": "Spider: Run Procedure",
}
for path, display in scriptNames.items():
scriptId = scriptService.getScriptID(path)
if scriptId and scriptId > 0:
s = {}
s["name"] = display
s["id"] = scriptId
scripts.append(s)
if not image:
return render_to_response("webemdb/data/image.html", {"image": image, "scripts": scripts})
default_z = image.getSizeZ() / 2
return render_to_response("webemdb/data/image.html", {"image": image, "scripts": scripts, "default_z": default_z})
def dataset(request, datasetId, conn=None, **kwargs):
"""
Shows the thumbnails in a dataset, provides a link back to EMDB entry (project)
"""
dataset = conn.getObject("Dataset", datasetId)
entryId = None
# look for parent project that has EMDB entry name (EMDB ID)
for p in dataset.listParents():
try:
emdbId = long(p.getName())
entryId = str(emdbId)
break
except:
pass
# add some scripts that we can run on a dataset
scriptService = conn.getScriptService()
scripts = []
scriptNames = {
"/EMAN2/Nonlinear_Anisotropic_Diffusion.py":
"IMOD: Nonlinear Anisotropic Diffusion",
"/EMAN2/Segger_Segmentation.py": "Segger: Segmentation",
"/EMAN2/Eman_Filters.py": "EMAN2: Filtering",
"/EMAN2/Ctf_Correction.py": "EMAN2: CTF Correction",
"/EMAN2/Run_Spider_Procedure.py": "Spider: Run Procedure"
}
for path, display in scriptNames.items():
scriptId = scriptService.getScriptID(path)
if scriptId and scriptId > 0:
s = {}
s["name"] = display
s["id"] = scriptId
scripts.append(s)
# gets list of {"id":annotationId, "name":fileName, "text":fileText} for .spf files
spfFiles = getSpfFiles(conn.getQueryService(), conn.createRawFileStore())
return render_to_response(
'webemdb/data/dataset.html', {
'dataset': dataset,
'entryId': entryId,
'scripts': scripts,
'spfFiles': spfFiles
})
def dataset(request, datasetId):
"""
Shows the thumbnails in a dataset, provides a link back to EMDB entry (project)
"""
conn = getConnection(request)
dataset = conn.getObject("Dataset", datasetId)
entryId = None
# look for parent project that has EMDB entry name (EMDB ID)
for p in dataset.listParents():
try:
emdbId = long(p.getName())
entryId = str(emdbId)
break
except:
pass
# add some scripts that we can run on a dataset
scriptService = conn.getScriptService()
scripts = []
scriptNames = {
"/EMAN2/Nonlinear_Anisotropic_Diffusion.py": "IMOD: Nonlinear Anisotropic Diffusion",
"/EMAN2/Segger_Segmentation.py": "Segger: Segmentation",
"/EMAN2/Eman_Filters.py": "EMAN2: Filtering",
"/EMAN2/Ctf_Correction.py": "EMAN2: CTF Correction",
"/EMAN2/Run_Spider_Procedure.py": "Spider: Run Procedure",
}
for path, display in scriptNames.items():
scriptId = scriptService.getScriptID(path)
if scriptId and scriptId > 0:
s = {}
s["name"] = display
s["id"] = scriptId
scripts.append(s)
# gets list of {"id":annotationId, "name":fileName, "text":fileText} for .spf files
spfFiles = getSpfFiles(conn.getQueryService(), conn.createRawFileStore())
return render_to_response(
"webemdb/data/dataset.html", {"dataset": dataset, "entryId": entryId, "scripts": scripts, "spfFiles": spfFiles}
)
def image(request, imageId, conn=None, **kwargs):
"""
Shows an image preview (single plane), Name, Description etc. links to datasets.
"""
image = conn.getObject("Image", imageId)
scriptService = conn.getScriptService()
scripts = []
scriptNames = {
"/EMAN2/Nonlinear_Anisotropic_Diffusion.py":
"IMOD: Nonlinear Anisotropic Diffusion",
"/EMAN2/Segger_Segmentation.py": "Segger: Segmentation",
"/EMAN2/Eman_Filters.py": "EMAN2: Filtering",
"/EMAN2/Ctf_Correction.py": "EMAN2: CTF Correction",
"/EMAN2/Run_Spider_Procedure.py": "Spider: Run Procedure"
}
for path, display in scriptNames.items():
scriptId = scriptService.getScriptID(path)
if scriptId and scriptId > 0:
s = {}
s["name"] = display
s["id"] = scriptId
scripts.append(s)
if not image:
return render_to_response('webemdb/data/image.html', {
'image': image,
"scripts": scripts
})
default_z = image.getSizeZ() / 2
return render_to_response('webemdb/data/image.html', {
'image': image,
"scripts": scripts,
"default_z": default_z
})
