Merge e39a45b into 3463ba8

deepcell_label/blueprints.py

@@ -25,7 +25,7 @@
 from deepcell_label.label import TrackEdit, ZStackEdit
 from deepcell_label.models import Project
 # from deepcell_label import loaders
-from deepcell_label import url_loaders
+from deepcell_label import loaders
 from deepcell_label import exporters
 from deepcell_label.config import S3_INPUT_BUCKET, S3_OUTPUT_BUCKET
 
@@ -38,7 +38,7 @@ def health():
     return jsonify({'message': 'success'}), 200
 
 
-@bp.errorhandler(url_loaders.InvalidExtension)
+@bp.errorhandler(loaders.InvalidExtension)
 def handle_invalid_extension(error):
     response = jsonify(error.to_dict())
     response.status_code = error.status_code
@@ -212,6 +212,18 @@ def get_project(token):
 #                             loader.path, timeit.default_timer() - start)
 #     return jsonify({'projectId': project.token})
 
+@bp.route('/api/project/dropped', methods=['POST'])
+def create_project_from_dropped_file():
+    """
+    Create a new Project from drag & dropped file.
+    """
+    start = timeit.default_timer()
+    loader = loaders.FileLoader(request)
+    project = Project.create(loader)
+    current_app.logger.info('Created project from %s in %s s.',
+                            loader.path, timeit.default_timer() - start)
+    return jsonify({'projectId': project.token})
+
 
 @bp.route('/api/project', methods=['POST'])
 def create_project_from_url():
@@ -220,17 +232,17 @@ def create_project_from_url():
     """
     start = timeit.default_timer()
     url_form = request.form
-    loader = url_loaders.Loader(url_form)
+    loader = loaders.URLLoader(url_form)
     project = Project.create(loader)
     current_app.logger.info('Created project from %s in %s s.',
-                            loader.url, timeit.default_timer() - start)
+                            loader.path, timeit.default_timer() - start)
     return jsonify({'projectId': project.token})
 
 
-@bp.route('/downloadproject/<token>', methods=['GET'])
+@bp.route('/api/download/<token>', methods=['GET'])
 def download_project(token):
     """
-    Download a .trk/.npz file from a DeepCell Label project.
+    Download a DeepCell Label project as a .npz file
     """
     project = Project.get(token)
     if not project:

deepcell_label/blueprints_test.py

@@ -4,8 +4,9 @@
 
 import pytest
 import numpy as np
+from skimage.external.tifffile import TiffWriter
+from PIL import Image
 
-# from flask_sqlalchemy import SQLAlchemy
 
 from deepcell_label import models
 from deepcell_label.conftest import DummyLoader
@@ -84,11 +85,40 @@ def test_redo(client):
 
 
 def test_create_project(client, mocker):
-    mocker.patch('deepcell_label.blueprints.url_loaders.Loader', lambda *args: DummyLoader())
+    mocker.patch('deepcell_label.blueprints.loaders.URLLoader', lambda *args: DummyLoader())
     response = client.post(f'/api/project')
     assert response.status_code == 200
 
 
+def test_create_project_dropped_npz(client):
+    npz = io.BytesIO()
+    np.savez(npz, X=np.zeros((1, 1, 1, 1)), y=np.ones((1, 1, 1, 1)))
+    npz.seek(0)
+    data = {'file': (npz, 'test.npz')}
+    response = client.post(f'/api/project/dropped', data=data, content_type='multipart/form-data')
+    assert response.status_code == 200
+
+
+def test_create_project_dropped_tiff(client):
+    tifffile = io.BytesIO()
+    with TiffWriter(tifffile) as writer:
+        writer.save(np.zeros((1, 1, 1, 1)))
+        tifffile.seek(0)
+    data = {'file': (tifffile, 'test.tiff')}
+    response = client.post(f'/api/project/dropped', data=data, content_type='multipart/form-data')
+    assert response.status_code == 200
+
+
+def test_create_project_dropped_png(client):
+    png = io.BytesIO()
+    img = Image.fromarray(np.zeros((1, 1)), mode='L')
+    img.save(png, format="png")
+    png.seek(0)
+    data = {'file': (png, 'test.png')}
+    response = client.post(f'/api/project/dropped', data=data, content_type='multipart/form-data')
+    assert response.status_code == 200
+
+
 def test_get_project(client):
     project = models.Project.create(DummyLoader())
     response = client.get(f'/api/project/{project.token}')

deepcell_label/conftest.py

@@ -9,7 +9,7 @@
 from unittest.mock import MagicMock
 
 from deepcell_label import create_app  # pylint: disable=C0413
-from deepcell_label.url_loaders import Loader
+from deepcell_label.loaders import Loader
 
 
 # flask-sqlalchemy fixtures from http://alexmic.net/flask-sqlalchemy-pytest/
@@ -21,9 +21,8 @@
 
 # TODO: Could this become a fixture?
 class DummyLoader(Loader):
-    def __init__(self, raw=None, labels=None, cell_info=None, url='test.npz'):
-        DummyLoader.load = MagicMock()  # monkeypatch to avoid network requests
-        super().__init__(url_form={'url': url})
+    def __init__(self, raw=None, labels=None, cell_info=None, path='test.npz'):
+        super().__init__()
 
         if raw is None:
             raw = np.zeros((1, 1, 1, 1))
@@ -33,6 +32,7 @@ def __init__(self, raw=None, labels=None, cell_info=None, url='test.npz'):
         elif labels.shape != raw.shape:
             raw = np.zeros(labels.shape)
 
+        self.path = path
         self.raw_array = raw
         self.label_array = labels
         self.add_semantic_labels()  # computes cell_ids

deepcell_label/exporters_test.py

@@ -12,7 +12,7 @@
 def npz_exporter(app, db_session):
     with app.app_context():
         db_session.autoflush = False
-        project = models.Project.create(DummyLoader(url='test.npz'))
+        project = models.Project.create(DummyLoader(path='test.npz'))
         exporter = exporters.Exporter(project)
         return exporter
 
@@ -21,7 +21,7 @@ def npz_exporter(app, db_session):
 def trk_exporter(app, db_session):
     with app.app_context():
         db_session.autoflush = False
-        project = models.Project.create(DummyLoader(url='test.trk'))
+        project = models.Project.create(DummyLoader(path='test.trk'))
         exporter = exporters.Exporter(project)
         return exporter
 

deepcell_label/label_test.py

@@ -396,7 +396,7 @@ class TestTrackEdit():
 
     def test_track_add_cell_info(self):
         labels = np.zeros((1, 1, 1, 1))
-        project = models.Project.create(DummyLoader(labels=labels, url='test.trk'))
+        project = models.Project.create(DummyLoader(labels=labels, path='test.trk'))
         edit = label.TrackEdit(project)
         tracks = edit.tracks
 
@@ -419,7 +419,7 @@ def test_track_add_cell_info(self):
     def test_add_cell_info_multiple_frames(self):
         num_frames = 5
         labels = np.zeros((num_frames, 1, 1, 1))
-        project = models.Project.create(DummyLoader(labels=labels, url='test.trk'))
+        project = models.Project.create(DummyLoader(labels=labels, path='test.trk'))
         edit = label.TrackEdit(project)
         tracks = edit.tracks
 
@@ -443,7 +443,7 @@ def test_action_new_track_first_frame_of_track(self, app):
         """A new track on the first frame a label appears does nothing."""
         # two 1x1 frames with one feature; cell starts on second frame
         labels = np.reshape([0, 1], (2, 1, 1, 1))
-        project = models.Project.create(DummyLoader(labels=labels, url='test.trk'))
+        project = models.Project.create(DummyLoader(labels=labels, path='test.trk'))
         cell = 1
         frame = 1
         feature = 0
@@ -462,7 +462,7 @@ def test_action_new_track(self, app):
         """Create a new track on the second frame of a label."""
         # two 1x1 frames with one feature; cell appears in both frames
         labels = np.reshape([1, 1], (2, 1, 1, 1))
-        project = models.Project.create(DummyLoader(labels=labels, url='test.trk'))
+        project = models.Project.create(DummyLoader(labels=labels, path='test.trk'))
         cell = 1
         frame = 1
         feature = 0