Example #1
0
def generate_intensity():
    """Generates an intensity data file related to some user action.

    Clear: clear the old intensity mapping
    Cluster: intensity mapping associated with a topic cluster
    Word: intensity mapping associated with a particular word
    Study: intensity mapping associated with a study cluster"""

    clicked_on = request.args.get("options")

    if clicked_on == "clear":

        intensities_by_location = {}

    elif clicked_on == "cluster" or clicked_on == "word":

        if clicked_on == "cluster":

            cluster = request.args.get("cluster")
            word = TermCluster.get_words_in_cluster(cluster)

        else:

            word = request.args.get("word")

        studies = StudyTerm.get_by_word(word)

        # Create a dictionary of {pmid: frequency} values
        frequencies_by_pmid, max_intensity = organize_frequencies_by_study(studies)
        pmids = frequencies_by_pmid.keys()

        # Get the activations for the keys of the dictionary
        activations = Activation.get_activations_from_studies(pmids)

        # Assemble the final dictionary of {location:intensity} values, scaling
        # each value as we go
        intensities_by_location = scale_frequencies_by_loc(activations, max_intensity, frequencies_by_pmid)

    elif clicked_on == "study":

        pmid = request.args.get("pmid")
        study = Study.get_study_by_pmid(pmid)

        # Look for cluster-mate studies
        cluster_mates = study.get_cluster_mates()

        # Get (location, study count) tuples from db
        activations = Activation.get_location_count_from_studies(cluster_mates)

        # Scale study counts in preparation for intensity mapping
        intensities_by_location = scale_study_counts(activations)

        print "Found intensities: ", intensities_by_location

    # Assemble the intensity map
    intensity_vals = generate_intensity_map(intensities_by_location)

    return intensity_vals
Example #2
0
def generate_word_d3():
    """ Returns JSON with a word as the root node."""
    # TO DO Adding word validation and then extra tests to tests.py

    word = request.args.get("word")
    clusters = TermCluster.get_top_clusters(word, n=25)

    root_dict = {"name": "", "children": []}

    for cluster in clusters:
        root_dict["children"].append({"name": cluster, "children": [{"name": word, "size": 40000}]})

    return jsonify(root_dict)
Example #3
0
def generate_topic_d3():
    """Returns JSON with a topic cluster as the root node."""
    # TO DO Adding cluster ID validation and then extra tests to tests.py

    cluster_id = request.args.get("cluster")
    words = TermCluster.get_words_in_cluster(cluster_id)

    root_dict = {"name": "", "children": []}

    for word in words:
        root_dict["children"].append({"name": "", "children": [{"name": word, "size": 40000}]})

    return jsonify(root_dict)
Example #4
0
def generate_citations(radius=3):
    """Returns a list of text citations associated with some location, word
    or topic (cluster)."""

    clicked_on = request.args.get("options")

    if clicked_on == "location":
        x_coord = float(request.args.get("xcoord"))
        y_coord = float(request.args.get("ycoord"))
        z_coord = float(request.args.get("zcoord"))

        pmids = Activation.get_pmids_from_xyz(x_coord, y_coord, z_coord, radius)

    elif clicked_on == "word":
        word = request.args.get("word")

        # Get the pmids for a word
        pmids = StudyTerm.get_pmid_by_term(word)

    elif clicked_on == "cluster":
        cluster = request.args.get("cluster")

        # Get the words for a cluster
        # Then get the top studies for the words
        words = TermCluster.get_words_in_cluster(cluster)
        pmids = StudyTerm.get_pmid_by_term(words)

    elif clicked_on == "study":

        pmid = request.args.get("pmid")
        study = Study.get_study_by_pmid(pmid)

        # Look for cluster-mate studies
        pmids = study.get_cluster_mates()

    citations = Study.get_references(pmids)

    return jsonify(citations)
Example #5
0
def generate_d3(radius=3):
    """ Returns JSON with xyz at the root node.

    Test with parameters: 40, -45, -25    (Fusiform face area)
    """

    clicked_on = request.args.get("options")

    if clicked_on == "location":

        x_coord = float(request.args.get("xcoord"))
        y_coord = float(request.args.get("ycoord"))
        z_coord = float(request.args.get("zcoord"))

        pmids = Activation.get_pmids_from_xyz(x_coord, y_coord, z_coord, radius)
        scale = 70000
        # Get [(wd, freq), ...] and [wd1, wd2] for most frequent words

    elif clicked_on == "study":

        pmid = request.args.get("pmid")
        study = Study.get_study_by_pmid(pmid)
        pmids = study.get_cluster_mates()
        scale = 30000

    terms_for_dict, words = StudyTerm.get_terms_by_pmid(pmids)
    # Optional: transform the terms
    # Get the top clusters
    top_clusters = TermCluster.get_top_clusters(words)
    # Get the cluster-word associations
    associations = TermCluster.get_word_cluster_pairs(top_clusters, words)

    # Make the root node:
    root_dict = {"name": "", "children": []}

    # Build the terminal nodes (leaves) first using (wd, freq) tuples
    # Output: {word: {'name': word, 'size': freq}, word2: ... }
    leaves = {}

    for (word, freq) in terms_for_dict:
        if word not in leaves:
            leaves[word] = {"name": word, "size": freq * scale}
        else:
            leaves[word]["size"] += freq * scale

    # Embed the leaves in the clusters:
    # Output: {cluster_id: {'name': ID, 'children': [...]}, ... }
    clusters = {}

    for (cluster_id, word) in associations:
        if cluster_id not in clusters:
            clusters[cluster_id] = {"name": cluster_id, "children": [leaves[word]]}
        else:
            clusters[cluster_id]["children"].append(leaves[word])

    # Put the clusters in the root dictionary
    # Output: {'name': root, children: [{'name': id, 'children': []}, ...]
    for cluster in top_clusters:
        root_dict["children"].append(clusters[cluster])

    return jsonify(root_dict)