Service-based support for summarization

pyrivet/rivet.py

@@ -9,12 +9,17 @@
 import shutil
 import numpy as np
 import scipy.spatial.distance as distance
+import json
 from typing import List, Tuple
 
 """An interface for rivet_console, using the command line
 and subprocesses."""
 
 rivet_executable = 'rivet_console'
+rivet_client = 'rivet-client'
+
+"""If set, use the rivet-client to run jobs on a remote server"""
+server_url = os.getenv("RIVET_SERVER")
 
 
 class PointCloud:
@@ -215,15 +220,19 @@ def barcodes(bytes, slices):
 
 
 def _rivet_name(base, homology, x, y):
-    output_name = base + (".H%d_x%d_y%d.rivet" % (homology, x, y))
+    output_name = base.strip() + (".H%d_x%d_y%d.rivet" % (homology, x, y))
     return output_name
 
 
-def compute_file(input_name, output_name=None, homology=0, x=0, y=0):
+def compute_file(input_name, output_name=None, homology=0, x=0, y=0, threads=1):
     if not output_name:
         output_name = _rivet_name(input_name, homology, x, y)
-    cmd = "%s %s %s -H %d -x %d -y %d -f msgpack" % \
-          (rivet_executable, input_name, output_name, homology, x, y)
+    if server_url:
+        cmd = "%s %s %s -H %d -x %d -y %d --redis %s --threads %d" % \
+              (rivet_client, input_name, output_name, homology, x, y, server_url, threads)
+    else:
+        cmd = "%s %s %s -H %d -x %d -y %d -f msgpack --num_threads %s" % \
+              (rivet_executable, input_name, output_name, homology, x, y, threads)
     subprocess.check_output(shlex.split(cmd))
     return output_name
 
@@ -254,6 +263,82 @@ def bounds_file(name):
     return parse_bounds(subprocess.check_output(shlex.split(cmd)).split(b'\n'))
 
 
+class Summary:
+    def __init__(self, invariants, structure, slices, barcodes, bounds):
+        self.invariants = invariants
+        self.structure = structure
+        self.slices = slices
+        self.barcodes = barcodes,
+        self.bounds = bounds
+
+
+def summarize(saveable, homology=0, x=0, y=0, slices=None, bounds=False, structure=False, return_invariants=False, threads=1):
+    """Computes module invariants for the given dataset, and queries them according the the parameters."""
+    if not server_url:
+        raise NotImplementedError
+
+    with TempDir() as dir:
+        input_path = os.path.join(dir, 'input.txt')
+        output_path = os.path.join(dir, 'output.rivet')
+        slices_path = os.path.join(dir, 'slices.txt')
+        bounds_path = output_path + '.bounds.json'
+        structure_path = output_path + '.structure.json'
+        barcodes_path = output_path + '.barcodes.json'
+        with open(input_path, 'wt') as input:
+            saveable.save(input)
+        cmd = "%s %s %s -H %d -x %d -y %d --redis %s --threads %d" % \
+              (rivet_client, input_path, output_path, homology, x, y, server_url, threads)
+        if slices:
+            with open(os.path.join(dir, 'slices.txt'), 'wt') as slice_temp:
+                for angle, offset in slices:
+                    slice_temp.write("%s %s\n" % (angle, offset))
+
+            cmd += (" --slices %s" % slices_path)
+        if structure:
+            cmd += " --structure"
+        if bounds:
+            cmd += " --bounds"
+        if not return_invariants:
+            cmd += " --no-invariants"
+        output = subprocess.check_output(shlex.split(cmd)).split(b'\n')
+        print(output)
+        if return_invariants:
+            invariants = open(output_path, 'rb').read()
+        else:
+            invariants = None
+        if bounds:
+            bounds = json.load(open(bounds_path))
+            bounds = Bounds((bounds['x_low'], bounds['y_low']), (bounds['x_high'], bounds['y_high']))
+        else:
+            bounds = None
+        if slices:
+            barcodes_json = json.load(open(barcodes_path))
+            barcodes = []
+            for bc in barcodes_json:
+                angle = bc['angle']
+                offset = bc['offset']
+                bars_array = np.array(bc['bars']['data']).reshape(bc['bars']['dim'])
+                bars = [barcode.Bar(row[0], row[1], row[2]) for row in bars_array]
+                barcodes.append(((angle, offset), barcode.Barcode(bars)))
+        else:
+            barcodes = []
+        if structure:
+            structure_json = json.load(open(structure_path))
+            x_grades = [fractions.Fraction(*num) for num in structure_json['x_grades']]
+            y_grades = [fractions.Fraction(*num) for num in structure_json['y_grades']]
+            graded_rank = None # TODO! Rust API doesn't have this right now.
+            xi_0 = [(val['x'], val['y'], val['betti_0']) for val in structure_json['points']
+                    if val['betti_0'] > 0]
+            xi_1 = [(val['x'], val['y'], val['betti_1']) for val in structure_json['points']
+                    if val['betti_1'] > 0]
+            xi_2 = [(val['x'], val['y'], val['betti_2']) for val in structure_json['points']
+                    if val['betti_2'] > 0]
+            structure = MultiBetti(Dimensions(x_grades, y_grades), graded_rank, xi_0, xi_1, xi_2)
+        else:
+            structure = None
+        return Summary(invariants, structure, slices, barcodes, bounds)
+
+
 class TempDir(os.PathLike):
     def __enter__(self):
         self.dirname = os.path.join(tempfile.gettempdir(),