Merge pull request #1654 from danforthcenter/parallelization_defaults

changing parallelization defaults

docs/parallel_config.md

@@ -64,8 +64,8 @@ Validate parameters/structure of configuration data.
 * **img_outdir**: (str, default = "."): path/name of output directory where images will be saved.
 
 
-* **tmp_dir**: (str, default = `None`): path/name of parent folder for the temporary directory, uses system default
-  temporary directory when `None`.
+* **tmp_dir**: (str, default = `"."`): path/name of parent folder for the temporary directory, defaults to the
+current working directory.
 
 
 * **start_date**: (str, default = `None`): start date used to filter images. Images will be analyzed that are newer 
@@ -107,15 +107,15 @@ for downstream analysis. The default, `filepath` will create groups of single im
 example of a multi-image group could be to pair VIS and NIR images (e.g. `["timestamp", "camera", "rotation"]`). Supported
 metadata terms are listed [here](pipeline_parallel.md).
 
-* **group_name** (str, default = `"imgtype"`): either a metadata term used to create a unique name for each image in an
+* **group_name** (str, default = `"auto"`): either a metadata term used to create a unique name for each image in an
 image group (created by `groupby`), or `"auto"` to generate a numbered image sequence `image1, image2, ...`. The resulting
 names are used to access individual image filepaths in a workflow.
 
 * **cleanup**: (bool, default =`True`): remove temporary job directory if `True`.
 
 
-* **append**: (bool, default = `True`): if `True` will append results to an existing json file. If `False`, will delete
-  previous results stored in the specified JSON file.
+* **append**: (bool, default = `False`): if `False`, will delete previous results stored in the specified JSON file.
+  If `True` will append results to an existing json file.
 
 
 * **cluster** (str, default = "LocalCluster"): LocalCluster will run PlantCV workflows on a single machine. All valid

docs/pipeline_parallel.md

@@ -99,7 +99,7 @@ Sample image filename: `cam1_16-08-06-16:45_el1100s1_p19.jpg`
     "filename_metadata": ["camera", "timestamp", "id", "other"],
     "workflow": "/home/mgehan/pat-edger/round1-python-pipelines/2016-08_pat-edger_brassica-cam1-splitimg.py",
     "img_outdir": "/shares/mgehan_share/raw_data/raw_image/2016-08_pat-edger/data/split-round1/split-cam1/output",
-    "tmp_dir": null,
+    "tmp_dir": "."",
     "start_date": null,
     "end_date": null,
     "imgformat": "jpg",
@@ -111,7 +111,7 @@ Sample image filename: `cam1_16-08-06-16:45_el1100s1_p19.jpg`
     "groupby": ["filepath"],
     "group_name": "auto",
     "cleanup": true,
-    "append": true,
+    "append": false,
     "cluster": "HTCondorCluster",
     "cluster_config": {
         "n_workers": 16,
@@ -175,7 +175,7 @@ in a list to the `filename_metadata` parameter.
     "filename_metadata": ["camera", "plantbarcode", "timestamp"],
     "workflow": "user-workflow.py",
     "img_outdir": "output_directory",
-    "tmp_dir": null,
+    "tmp_dir": ".",
     "start_date": null,
     "end_date": null,
     "imgformat": "jpg",
@@ -187,7 +187,7 @@ in a list to the `filename_metadata` parameter.
     "groupby": ["filepath"],
     "group_name": "auto",
     "cleanup": true,
-    "append": true,
+    "append": false,
     "cluster": "HTCondorCluster",
     "cluster_config": {
         "n_workers": 16,
@@ -227,7 +227,7 @@ To identify each image within our workflow, we will name them based on the `imgt
     "filename_metadata": ["imgtype", "timestamp", "id", "other"],
     "workflow": "/home/mgehan/pat-edger/round1-python-pipelines/2016-08_pat-edger_brassica-cam1-splitimg.py",
     "img_outdir": "/shares/mgehan_share/raw_data/raw_image/2016-08_pat-edger/data/split-round1/split-cam1/output",
-    "tmp_dir": null,
+    "tmp_dir": ".",
     "start_date": null,
     "end_date": null,
     "imgformat": "jpg",
@@ -239,7 +239,7 @@ To identify each image within our workflow, we will name them based on the `imgt
     "groupby": ["timestamp"],
     "group_name": "imgtype",
     "cleanup": true,
-    "append": true,
+    "append": false,
     "cluster": "HTCondorCluster",
     "cluster_config": {
         "n_workers": 16,

plantcv/parallel/__init__.py

@@ -21,7 +21,7 @@ def __init__(self):
         self.workflow = ""
         self.img_outdir = "./output_images"
         self.include_all_subdirs = True
-        self.tmp_dir = None
+        self.tmp_dir = "."
         self.start_date = None
         self.end_date = None
         self.imgformat = "png"
@@ -31,9 +31,9 @@ def __init__(self):
         self.writeimg = False
         self.other_args = {}
         self.groupby = ["filepath"]
-        self.group_name = "imgtype"
+        self.group_name = "auto"
         self.cleanup = True
-        self.append = True
+        self.append = False
         self.cluster = "LocalCluster"
         self.cluster_config = {
             "n_workers": 1,

tests/testdata/workflowconfig_template.json

@@ -5,7 +5,7 @@
     "include_all_subdirs": true,
     "workflow": "",
     "img_outdir": "./output_images",
-    "tmp_dir": null,
+    "tmp_dir": ".",
     "start_date": null,
     "end_date": null,
     "imgformat": "png",
@@ -15,9 +15,9 @@
     "writeimg": false,
     "other_args": {},
     "groupby": ["filepath"],
-    "group_name": "imgtype",
+    "group_name": "auto",
     "cleanup": true,
-    "append": true,
+    "append": false,
     "cluster": "LocalCluster",
     "cluster_config": {
         "n_workers": 1,