Mercurial > repos > bimib > cobraxy

comparison COBRAxy/flux_to_map.py @ 147:3fca9b568faf draft

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author bimib
date Wed, 06 Nov 2024 13:57:24 +0000
parents 41f35c2f0c7b
children 5683406a8cfd
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equal deleted inserted replaced
146:88cf4543e210 147:3fca9b568faf
20 import matplotlib.pyplot as plt 20 import matplotlib.pyplot as plt
21 21
22 ERRORS = [] 22 ERRORS = []
23 ########################## argparse ########################################## 23 ########################## argparse ##########################################
24 ARGS :argparse.Namespace 24 ARGS :argparse.Namespace
25 def process_args() -> argparse.Namespace: 25 def process_args(args:List[str] = None) -> argparse.Namespace:
26 """ 26 """
27 Interfaces the script of a module with its frontend, making the user's choices for various parameters available as values in code. 27 Interfaces the script of a module with its frontend, making the user's choices for various parameters available as values in code.
28 28
29 Args: 29 Args:
30 args : Always obtained (in file) from sys.argv 30 args : Always obtained (in file) from sys.argv
117 117
118 parser.add_argument( 118 parser.add_argument(
119 '-colorm', '--color_map', 119 '-colorm', '--color_map',
120 type = str, 120 type = str,
121 choices = ["jet", "viridis"]) 121 choices = ["jet", "viridis"])
122 122
123 args :argparse.Namespace = parser.parse_args() 123 parser.add_argument(
124 '-idop', '--output_path',
125 type = str,
126 default='result',
127 help = 'output path for maps')
128
129 args :argparse.Namespace = parser.parse_args(args)
124 args.net = True 130 args.net = True
125 131
126 return args 132 return args
127 133
128 ############################ dataset input #################################### 134 ############################ dataset input ####################################
641 f"{dataset1Name}_vs_{dataset2Name}" + (f" ({details})" if details else ""), 647 f"{dataset1Name}_vs_{dataset2Name}" + (f" ({details})" if details else ""),
642 # ^^^ yes this string is built every time even if the form is the same for the same 2 datasets in 648 # ^^^ yes this string is built every time even if the form is the same for the same 2 datasets in
643 # all output files: I don't care, this was never the performance bottleneck of the tool and 649 # all output files: I don't care, this was never the performance bottleneck of the tool and
644 # there is no other net gain in saving and re-using the built string. 650 # there is no other net gain in saving and re-using the built string.
645 ext, 651 ext,
646 prefix = "result") 652 prefix = ARGS.output_path)
647 653
648 FIELD_NOT_AVAILABLE = '/' 654 FIELD_NOT_AVAILABLE = '/'
649 def writeToCsv(rows: List[list], fieldNames :List[str], outPath :utils.FilePath) -> None: 655 def writeToCsv(rows: List[list], fieldNames :List[str], outPath :utils.FilePath) -> None:
650 fieldsAmt = len(fieldNames) 656 fieldsAmt = len(fieldNames)
651 with open(outPath.show(), "w", newline = "") as fd: 657 with open(outPath.show(), "w", newline = "") as fd:
920 min_flux_means = min(min_nonzero_abs(arr) for arr in means.values()) 926 min_flux_means = min(min_nonzero_abs(arr) for arr in means.values())
921 927
922 medians = {key: median/max_flux_medians for key, median in medians.items()} 928 medians = {key: median/max_flux_medians for key, median in medians.items()}
923 means = {key: mean/max_flux_means for key, mean in means.items()} 929 means = {key: mean/max_flux_means for key, mean in means.items()}
924 930
925 save_colormap_image(min_flux_medians, max_flux_medians, utils.FilePath("Color map median", ext=utils.FileFormat.PNG, prefix="result"), colormap) 931 save_colormap_image(min_flux_medians, max_flux_medians, utils.FilePath("Color map median", ext=utils.FileFormat.PNG, prefix=ARGS.output_path), colormap)
926 save_colormap_image(min_flux_means, max_flux_means, utils.FilePath("Color map mean", ext=utils.FileFormat.PNG, prefix="result"), colormap) 932 save_colormap_image(min_flux_means, max_flux_means, utils.FilePath("Color map mean", ext=utils.FileFormat.PNG, prefix=ARGS.output_path), colormap)
927 933
928 cmap = plt.get_cmap(colormap) 934 cmap = plt.get_cmap(colormap)
929 935
930 for key in class_pat: 936 for key in class_pat:
931 # Create color mappings for median and mean 937 # Create color mappings for median and mean
979 key (str): The key identifying the specific map. 985 key (str): The key identifying the specific map.
980 986
981 Returns: 987 Returns:
982 None 988 None
983 """ 989 """
984 svgFilePath = utils.FilePath(f"SVG Map {map_type} - {key}", ext=utils.FileFormat.SVG, prefix="result") 990 svgFilePath = utils.FilePath(f"SVG Map {map_type} - {key}", ext=utils.FileFormat.SVG, prefix=ARGS.output_path)
985 utils.writeSvg(svgFilePath, metabMap) 991 utils.writeSvg(svgFilePath, metabMap)
986 if ARGS.generate_pdf: 992 if ARGS.generate_pdf:
987 pngPath = utils.FilePath(f"PNG Map {map_type} - {key}", ext=utils.FileFormat.PNG, prefix="result") 993 pngPath = utils.FilePath(f"PNG Map {map_type} - {key}", ext=utils.FileFormat.PNG, prefix=ARGS.output_path)
988 pdfPath = utils.FilePath(f"PDF Map {map_type} - {key}", ext=utils.FileFormat.PDF, prefix="result") 994 pdfPath = utils.FilePath(f"PDF Map {map_type} - {key}", ext=utils.FileFormat.PDF, prefix=ARGS.output_path)
989 convert_to_pdf(svgFilePath, pngPath, pdfPath) 995 convert_to_pdf(svgFilePath, pngPath, pdfPath)
990 if not ARGS.generate_svg: 996 if not ARGS.generate_svg:
991 os.remove(svgFilePath.show()) 997 os.remove(svgFilePath.show())
992 998
993 999
994 1000
995 1001
996 ############################ MAIN ############################################# 1002 ############################ MAIN #############################################
997 def main() -> None: 1003 def main(args:List[str] = None) -> None:
998 """ 1004 """
999 Initializes everything and sets the program in motion based on the fronted input arguments. 1005 Initializes everything and sets the program in motion based on the fronted input arguments.
1000 1006
1001 Returns: 1007 Returns:
1002 None 1008 None
1004 Raises: 1010 Raises:
1005 sys.exit : if a user-provided custom map is in the wrong format (ET.XMLSyntaxError, ET.XMLSchemaParseError) 1011 sys.exit : if a user-provided custom map is in the wrong format (ET.XMLSyntaxError, ET.XMLSchemaParseError)
1006 """ 1012 """
1007 1013
1008 global ARGS 1014 global ARGS
1009 ARGS = process_args() 1015 ARGS = process_args(args)
1010 1016
1011 if os.path.isdir('result') == False: os.makedirs('result') 1017 if os.path.isdir(ARGS.output_path) == False: os.makedirs(ARGS.output_path)
1012 1018
1013 core_map :ET.ElementTree = ARGS.choice_map.getMap( 1019 core_map :ET.ElementTree = ARGS.choice_map.getMap(
1014 ARGS.tool_dir, 1020 ARGS.tool_dir,
1015 utils.FilePath.fromStrPath(ARGS.custom_map) if ARGS.custom_map else None) 1021 utils.FilePath.fromStrPath(ARGS.custom_map) if ARGS.custom_map else None)
1016 # TODO: ^^^ ugly but fine for now, the argument is None if the model isn't custom because no file was given. 1022 # TODO: ^^^ ugly but fine for now, the argument is None if the model isn't custom because no file was given.