Merge pull request #15 from jburel/fix_version

Fix version
ome · May 15, 2020 · 77da0e1 · 77da0e1
2 parents 7a6062a + dcc7b40
commit 77da0e1
Show file tree

Hide file tree

Showing 7 changed files with 22 additions and 21 deletions.
diff --git a/binder/environment.yml b/binder/environment.yml
@@ -7,7 +7,7 @@ dependencies:
   - omero-py
   - pip
   - ilastik-dependencies-no-solvers
-  - ilastik-meta
+  - ilastik-meta==1.4.0b5
   - ipywidgets
   - zarr  # for scripts reading from S3
   - s3fs  # for scripts reading from S3

diff --git a/notebooks/pixel_classification.ipynb b/notebooks/pixel_classification.ipynb
@@ -35,7 +35,7 @@
     "from getpass import getpass\n",
     "from collections import OrderedDict\n",
     "\n",
-    "import ilastik_main\n",
+    "from ilastik import app\n",
     "from ilastik.applets.dataSelection.opDataSelection import PreloadedArrayDatasetInfo\n",
     "import ipywidgets as widgets"
    ]
@@ -76,7 +76,7 @@
     "conn = BlitzGateway(input(\"Username: \"),\n",
     "                    getpass(\"OMERO Password: \"),\n",
     "                    host=HOST, secure=True)\n",
-    "conn.connect()\n",
+    "print(conn.connect())\n",
     "conn.c.enableKeepAlive(60)"
    ]
   },
@@ -270,10 +270,10 @@
     "# Prepare ilastik\n",
     "os.environ[\"LAZYFLOW_THREADS\"] = \"2\"\n",
     "os.environ[\"LAZYFLOW_TOTAL_RAM_MB\"] = \"2000\"\n",
-    "args = ilastik_main.parse_args([])\n",
+    "args = app.parse_args([])\n",
     "args.headless = True\n",
     "args.project = model_file\n",
-    "shell = ilastik_main.main(args)\n",
+    "shell = app.main(args)\n",
     "\n",
     "images = itertools.islice(images, 2)\n",
     "for image in images:\n",

diff --git a/notebooks/pixel_classification_zarr.ipynb b/notebooks/pixel_classification_zarr.ipynb
@@ -39,7 +39,7 @@
     "from getpass import getpass\n",
     "from collections import OrderedDict\n",
     "\n",
-    "import ilastik_main\n",
+    "from ilastik import app\n",
     "from ilastik.applets.dataSelection.opDataSelection import PreloadedArrayDatasetInfo\n",
     "import ipywidgets as widgets\n",
     "# package for 3d visualization\n",
@@ -779,10 +779,10 @@
     "# Prepare ilastik\n",
     "os.environ[\"LAZYFLOW_THREADS\"] = \"2\"\n",
     "os.environ[\"LAZYFLOW_TOTAL_RAM_MB\"] = \"2000\"\n",
-    "args = ilastik_main.parse_args([])\n",
+    "args = app.parse_args([])\n",
     "args.headless = True\n",
     "args.project = model_file\n",
-    "shell = ilastik_main.main(args)\n",
+    "shell = app.main(args)\n",
     "\n",
     "values = itertools.islice(images, 2)\n",
     "for image in values:\n",

diff --git a/notebooks/pixel_classification_zarr_idr.ipynb b/notebooks/pixel_classification_zarr_idr.ipynb
@@ -37,7 +37,7 @@
     "\n",
     "from collections import OrderedDict\n",
     "\n",
-    "import ilastik_main\n",
+    "from ilastik import app\n",
     "from ilastik.applets.dataSelection.opDataSelection import PreloadedArrayDatasetInfo\n",
     "\n",
     "# package for 3d visualization\n",
@@ -809,10 +809,10 @@
     "# Prepare ilastik\n",
     "os.environ[\"LAZYFLOW_THREADS\"] = \"2\"\n",
     "os.environ[\"LAZYFLOW_TOTAL_RAM_MB\"] = \"2000\"\n",
-    "args = ilastik_main.parse_args([])\n",
+    "args = app.parse_args([])\n",
     "args.headless = True\n",
     "args.project = model_file\n",
-    "shell = ilastik_main.main(args)\n",
+    "shell = app.main(args)\n",
     "\n",
     "print('running ilastik using %s' % model_file)\n",
     "role_data_dict = OrderedDict(\n",

diff --git a/scripts/pixel_classification.py b/scripts/pixel_classification.py
@@ -30,7 +30,7 @@
 from getpass import getpass
 from collections import OrderedDict
 
-import ilastik_main
+from ilastik import app
 from ilastik.applets.dataSelection.opDataSelection import PreloadedArrayDatasetInfo  # noqa
 
 
@@ -105,10 +105,10 @@ def analyze(conn, images, model, new_dataset):
     # Prepare ilastik
     os.environ["LAZYFLOW_THREADS"] = "2"
     os.environ["LAZYFLOW_TOTAL_RAM_MB"] = "2000"
-    args = ilastik_main.parse_args([])
+    args = app.parse_args([])
     args.headless = True
     args.project = model
-    shell = ilastik_main.main(args)
+    shell = app.main(args)
     for image in images:
         input_data = load_numpy_array(image)
         # run ilastik headless

diff --git a/scripts/pixel_classification_zarr.py b/scripts/pixel_classification_zarr.py
@@ -22,6 +22,7 @@
 # Version: 1.0
 #
 
+import time
 import tempfile
 import tarfile
 import numpy
@@ -34,7 +35,7 @@
 from getpass import getpass
 from collections import OrderedDict
 
-import ilastik_main
+from ilastik import app
 from ilastik.applets.dataSelection.opDataSelection import PreloadedArrayDatasetInfo  # noqa
 
 
@@ -112,12 +113,12 @@ def analyze(conn, images, model, new_dataset, extension=".tar", resolution=0):
 
     os.environ["LAZYFLOW_THREADS"] = "2"
     os.environ["LAZYFLOW_TOTAL_RAM_MB"] = "2000"
-    args = ilastik_main.parse_args([])
+    args = app.parse_args([])
     args.headless = True
     args.project = model
     args.readonly = True
-    shell = ilastik_main.main(args)
-    import time
+    shell = app.main(args)
+
     start = time.time()
     for image in images:
         input_data = load_from_s3(image, path)

diff --git a/scripts/pixel_classification_zarr_parallel.py b/scripts/pixel_classification_zarr_parallel.py
@@ -33,7 +33,7 @@
 from getpass import getpass
 from collections import OrderedDict
 
-import ilastik_main
+from ilastik import app
 from ilastik.applets.dataSelection.opDataSelection import PreloadedArrayDatasetInfo  # noqa
 
 import time
@@ -68,11 +68,11 @@ def load_from_s3(image_id, resolution='0'):
 
 # Analyze-data
 def analyze(image_id, model):
-    args = ilastik_main.parse_args([])
+    args = app.parse_args([])
     args.headless = True
     args.project = model
     args.readonly = True
-    shell = ilastik_main.main(args)
+    shell = app.main(args)
     input_data = load_from_s3(image_id)
     # run ilastik headless
     data = OrderedDict([