Exemple #1
0
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})
Exemple #2
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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
        })
Exemple #3
0
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}
    )
Exemple #4
0
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
    })