diff --git a/docs/parallel_config.md b/docs/parallel_config.md index d45fb8477..631b1bf8b 100644 --- a/docs/parallel_config.md +++ b/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 diff --git a/docs/pipeline_parallel.md b/docs/pipeline_parallel.md index ce74ec07a..60f3c1f9f 100644 --- a/docs/pipeline_parallel.md +++ b/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, diff --git a/plantcv/parallel/__init__.py b/plantcv/parallel/__init__.py index ff94ae2af..faef77317 100644 --- a/plantcv/parallel/__init__.py +++ b/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, diff --git a/tests/testdata/workflowconfig_template.json b/tests/testdata/workflowconfig_template.json index 5393b86b4..7c7310e08 100644 --- a/tests/testdata/workflowconfig_template.json +++ b/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,