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comparison starting_modules.py @ 0:39006f6fd6bf draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
author bgruening
date Sat, 06 Feb 2021 10:06:16 +0000
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children 91560258e972
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-1:000000000000 0:39006f6fd6bf
1 import json
2 import sys
3
4 FOURSPACES = " "
5
6 input_json_path = sys.argv[1]
7
8 params = json.load(open(input_json_path, "r"))
9
10
11 def write_images():
12 filter_images = params['images']['filter_images']
13
14 _str = "\nImages:[module_num:1|svn_version:\\'Unknown\\'|variable_revision_number:2|show_window:False|notes:\\x5B\\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n"
15 _str += FOURSPACES + ":\n"
16 _str += FOURSPACES + "Filter images?:%s\n" % filter_images
17 _str += FOURSPACES + "Select the rule criteria:and (extension does isimage) (directory doesnot startwith \".\")\n"
18
19 return _str
20
21
22 def write_metadata():
23 metadata_extraction = params['metadata']['con_metadata_extraction']
24 extract = metadata_extraction['extract']
25
26 if 'extraction_method' in metadata_extraction:
27 method_count = len(metadata_extraction['extraction_method'])
28 else:
29 method_count = 1
30
31 _str = "\nMetadata:[module_num:2|svn_version:\\'Unknown\\'|variable_revision_number:4|show_window:False|notes:\\x5B\\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n"
32 _str += FOURSPACES + "Extract metadata?:%s\n" % extract
33
34 if extract == "No":
35 _str += FOURSPACES + "Metadata data type:Text\n"
36 _str += FOURSPACES + "Metadata types:{}\n"
37 _str += FOURSPACES + "Extraction method count:%d\n" % method_count
38 _str += FOURSPACES + "Metadata extraction method:Extract from file/folder names\n"
39 _str += FOURSPACES + "Regular expression to extract from file name:^(?P<Plate>.*)_(?P<Well>\x5BA-P\x5D\x5B0-9\x5D{2})_s(?P<Site>\x5B0-9\x5D)_w(?P<ChannelNumber>\x5B0-9\x5D)\n"
40 _str += FOURSPACES + "Regular expression to extract from folder name:(?P<Date>\x5B0-9\x5D{4}_\x5B0-9\x5D{2}_\x5B0-9\x5D{2})$\n"
41 _str += FOURSPACES + "Extract metadata from:All images\n"
42 _str += FOURSPACES + "Select the filtering criteria:and (file does contain \"\")\n"
43 _str += FOURSPACES + "Metadata file location:\n"
44 _str += FOURSPACES + "Match file and image metadata:\x5B\x5D\n"
45 _str += FOURSPACES + "Use case insensitive matching?:No\n"
46 else:
47 _str += FOURSPACES + "Metadata data type:Text\n" # default Text,not possible to select in Galaxy
48 _str += FOURSPACES + "Metadata types:{}\n"
49 _str += FOURSPACES + "Extraction method count:%d\n" % method_count
50
51 for methods in metadata_extraction["extraction_method"]:
52 _str += FOURSPACES + "Metadata extraction method:%s\n" % methods["metadata_extraction_method"]
53 _str += FOURSPACES + "Metadata source:%s\n" % methods["con_metadata_source"]["metadata_source"]
54
55 if "file_name_regex" in methods["con_metadata_source"]:
56 file_regex = methods["con_metadata_source"]["file_name_regex"]
57 folder_regex = "(?P<folderField1>.*)"
58 elif "folder_name_regex" in methods["con_metadata_source"]:
59 file_regex = "(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)"
60 folder_regex = methods["con_metadata_source"]["folder_name_regex"]
61 else:
62 # default regex
63 file_regex = "(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)"
64 folder_regex = "(?P<folderField1>.*)"
65
66 _str += FOURSPACES + "Regular expression to extract from file name:%s\n" % file_regex
67 _str += FOURSPACES + "Regular expression to extract from folder name:%s\n" % folder_regex
68
69 _str += FOURSPACES + "Extract metadata from:%s\n" % methods["con_metadata_extract_from"]["extract_metadata_from"]
70
71 if methods["con_metadata_extract_from"]["extract_metadata_from"] == "Images matching a rule":
72 rule_str = ""
73 for r in methods["con_metadata_extract_from"]["r_match"]:
74 if r["con_match"]["rule_type"] == "extension":
75 rule_str += " (" + r["con_match"]["rule_type"] + " " + r["con_match"]["operator"] + " " + \
76 r["con_match"]["match_type"] + ")"
77 else:
78 rule_str += " (" + r["con_match"]["rule_type"] + " " + r["con_match"]["operator"] + " " +\
79 r["con_match"]["contain"] + " \"" + r["con_match"]["match_value"] + "\")"
80
81 _str += FOURSPACES + "Select the filtering criteria:" + methods["con_metadata_extract_from"]["match_all_any"] + rule_str + "\n"
82 else:
83 _str += FOURSPACES + "Select the filtering criteria:and (file does contain \"\")\n" # this line is required even if it's not used
84
85 _str += FOURSPACES + "Metadata file location:\n"
86 _str += FOURSPACES + "Match file and image metadata:\x5B\x5D\n"
87 _str += FOURSPACES + "Use case insensitive matching?:No\n"
88
89 return _str
90
91
92 def write_nameandtypes():
93 nameandtypes = params['nameandtypes']
94 assign_a_name = nameandtypes['con_assign_a_name_to']['assign_a_name_to']
95
96 if "con_select_image_type" in nameandtypes['con_assign_a_name_to']:
97 con_set_intensity = nameandtypes['con_assign_a_name_to']['con_select_image_type']['con_set_intensity']
98 max_intensity = con_set_intensity['maximum_intensity'] if "maximum_intensity" in con_set_intensity else 255.0
99 else:
100 max_intensity = 255.0
101
102 pixel_space = nameandtypes['pixel_space']
103
104 rule_count = len(nameandtypes['con_assign_a_name_to']['r_match_rule']) if "r_match_rule" in nameandtypes['con_assign_a_name_to'] else 1
105
106 process_3d = nameandtypes['pixel_space']['process_3d']
107 x_spacing = 1.0 if "x_spacing" not in pixel_space else pixel_space["x_spacing"]
108 y_spacing = 1.0 if "y_spacing" not in pixel_space else pixel_space["y_spacing"]
109 z_spacing = 1.0 if "z_spacing" not in pixel_space else pixel_space["z_spacing"]
110
111 _str = "\nNamesAndTypes:[module_num:3|svn_version:\\'Unknown\\'|variable_revision_number:8|show_window:False|notes:\\x5B\\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\\'\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n"
112
113 _str += FOURSPACES + "Assign a name to:%s\n" % assign_a_name
114
115 if assign_a_name == "All images":
116 _str += FOURSPACES + "Select the image type:%s\n" % nameandtypes['con_assign_a_name_to']['con_select_image_type']['select_image_type']
117 _str += FOURSPACES + "Name to assign these images:%s\n" % nameandtypes['con_assign_a_name_to']['name_to_assign']
118 _str += FOURSPACES + "Match metadata:[]\n"
119
120 _str += FOURSPACES + "Image set matching method:Order\n"
121 _str += FOURSPACES + "Set intensity range from:%s\n" % con_set_intensity['set_intensity_range_from']
122 _str += FOURSPACES + "Assignments count:%s\n" % rule_count
123 _str += FOURSPACES + "Single images count:0\n"
124 _str += FOURSPACES + "Maximum intensity:%.1f\n" % max_intensity
125 _str += FOURSPACES + "Process as 3D?:%s\n" % process_3d
126
127 else:
128 # the below lines are not relevant to "images matching rules", but needed in pipeline file
129 _str += FOURSPACES + "Select the image type:Grayscale image\n"
130 _str += FOURSPACES + "Name to assign these images:DNA\n"
131 _str += FOURSPACES + "Match metadata:[]\n"
132
133 _str += FOURSPACES + "Image set matching method:%s\n" % nameandtypes['con_assign_a_name_to']['matching_method']
134 _str += FOURSPACES + "Set intensity range from:Image metadata\n"
135 _str += FOURSPACES + "Assignments count:%d\n" % rule_count
136 _str += FOURSPACES + "Single images count:0\n"
137 _str += FOURSPACES + "Maximum intensity:%.1f\n" % max_intensity
138 _str += FOURSPACES + "Process as 3D?:%s\n" % process_3d
139
140 _str += FOURSPACES + "Relative pixel spacing in X:%.1f\n" % x_spacing
141 _str += FOURSPACES + "Relative pixel spacing in Y:%.1f\n" % y_spacing
142 _str += FOURSPACES + "Relative pixel spacing in Z:%.1f\n" % z_spacing
143
144 if assign_a_name == "Images matching rules":
145 for rule in nameandtypes["con_assign_a_name_to"]["r_match_rule"]:
146
147 rule_str = ""
148 if len(rule["r_match"]) > 0:
149 for r in rule["r_match"]:
150 if r["con_match"]["rule_type"] == "file" or r["con_match"]["rule_type"] == "directory":
151 rule_str += " (" + r["con_match"]["rule_type"] + " " + r["con_match"]["operator"] + " " + \
152 r["con_match"]["contain"] + " \"" + r["con_match"]["match_value"] + "\")"
153 else:
154 rule_str += " (" + r["con_match"]["rule_type"] + " " + r["con_match"]["operator"] + " " + \
155 r["con_match"]["match_type"] + ")"
156 else:
157 rule_str = " (file does contain \"\")" # need to have a value even if it is not used
158
159 _str += FOURSPACES + "Select the rule criteria:" + rule["match_all_any"] + rule_str + "\n"
160
161 img_or_obj = rule["con_select_image_type"]["select_image_type"]
162
163 if img_or_obj == "Objects":
164 _str += FOURSPACES + "Name to assign these images:DNA\n"
165 _str += FOURSPACES + "Name to assign these objects:%s\n" % rule["con_select_image_type"]["name_to_assign"]
166 else:
167 _str += FOURSPACES + "Name to assign these images:%s\n" % rule["con_select_image_type"]["name_to_assign"]
168 _str += FOURSPACES + "Name to assign these objects:Cell\n"
169
170 _str += FOURSPACES + "Select the image type:%s\n" % img_or_obj
171
172 intensity_range = "Image metadata" # default value
173 if img_or_obj == "Grayscale image" or img_or_obj == "Color image":
174 intensity_range = rule["con_select_image_type"]["con_set_intensity"]["set_intensity_range_from"]
175
176 _str += FOURSPACES + "Set intensity range from:%s\n" % intensity_range
177
178 if intensity_range == "Manual":
179 _str += FOURSPACES + "Maximum intensity:%s\n" % rule["con_select_image_type"]["con_set_intensity"]["maximum_intensity"]
180 else:
181 _str += FOURSPACES + "Maximum intensity:255.0\n"
182
183 return _str
184
185
186 def write_groups():
187 groups = params['groups']
188
189 _str = "\nGroups:[module_num:4|svn_version:\\'Unknown\\'|variable_revision_number:2|show_window:False|notes:\\x5B\\\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\\'\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n"
190
191 group_images = groups["con_groups"]["group_images"]
192
193 _str += FOURSPACES + "Do you want to group your images?:%s\n" % group_images
194 _str += FOURSPACES + "grouping metadata count:1\n"
195
196 if group_images == "Yes":
197 _str += FOURSPACES + "Metadata category:%s\n" % groups["con_groups"]["group_category"]
198 else:
199 _str += FOURSPACES + "Metadata category:None\n"
200
201 return _str
202
203
204 with open("output.cppipe", "w") as f:
205 headers = ["CellProfiler Pipeline: http://www.cellprofiler.org\n",
206 "Version:3\n",
207 "DateRevision:319\n",
208 "GitHash:\n",
209 "ModuleCount:4\n",
210 "HasImagePlaneDetails:False",
211 "\n"]
212
213 f.writelines(headers)
214
215 img_str = write_images()
216 metadata_str = write_metadata()
217 nameandtypes_str = write_nameandtypes()
218 groups_str = write_groups()
219
220 output_str = img_str + metadata_str + nameandtypes_str + groups_str
221
222 f.write(output_str)
223 f.close()