Merge pull request #117 from imodpasteur/transform-headers

Transform headers

shareloc_utils/VERSION

@@ -1,3 +1,3 @@
 {
-    "version": "0.1.8"
+    "version": "0.1.9"
 }

shareloc_utils/batch_download.py

@@ -12,7 +12,7 @@
 
 from tqdm import tqdm
 from shareloc_utils.smlm_file import read_smlm_file
-
+from shareloc_utils.formats import supported_text_formats
 
 class DownloadProgressBar(tqdm):
     def update_to(self, b=1, bsize=1, tsize=None):
@@ -32,10 +32,15 @@ def resolve_url(rdf_url, path):
     return urljoin(os.path.dirname(rdf_url) + "/", path)
 
 
-def convert_smlm(file_path, delimiter=",", extension=".csv"):
+def convert_smlm(file_path, delimiter=",", extension=".csv", format="ThunderSTORM (csv)"):
     smlm_info = read_smlm_file(file_path)
     converted_files = []
     table_count = len(smlm_info["files"])
+    format_config = supported_text_formats[format];
+    header_transform = {}
+    for k, v in format_config["header_transform"].items():
+        header_transform[v]=k
+
     for tbi, file_info in enumerate(smlm_info["files"]):
         cols = file_info["cols"]
         rows = file_info["rows"]
@@ -46,7 +51,7 @@ def convert_smlm(file_path, delimiter=",", extension=".csv"):
         )
         with open(fp, "w") as f:
             for i in range(cols):
-                f.write(headers[i] + (delimiter if i < cols - 1 else "\n"))
+                f.write((header_transform.get(headers[i], headers[i])) + (delimiter if i < cols - 1 else "\n"))
             for i in tqdm(range(rows), total=rows):
                 for j in range(cols):
                     f.write(

shareloc_utils/formats.py

@@ -0,0 +1,141 @@
+
+supported_text_formats = {
+    "ThunderSTORM (csv)": {
+        # Required
+        "type": "table",
+        "extension": ".csv",
+        "mode": "text",
+        "dtype": "float32",
+        "delimiter": ",",
+        "comments": "",
+        # specify which row is the header, set to -1 if there is no header
+        "header_row": 0,
+        # specify how to transform the headers to the standard header defined in smlm format,
+        "header_transform": { "x [nm]": "x", "y [nm]": "y", "z [nm]": "z", "uncertainty_xy [nm]": "uncertainty_xy", "uncertainty_z [nm]": "uncertainty_z" },
+
+        # Optional
+        "name": "ThunderSTORM (csv)",
+        "description": "a csv format used in thunderSTORM"
+    },
+    "ThunderSTORM (xls)": {
+        # Required
+        "type": "table",
+        "extension": ".xls",
+        "mode": "text",
+        "dtype": "float32",
+        "delimiter": "\t",
+        "comments": "",
+        # specify which row is the header, set to -1 if there is no header
+        "header_row": 0,
+        # specify how to transform the headers to the standard header defined in smlm format,
+        "header_transform": { "x [nm]": "x", "y [nm]": "y", "z [nm]": "z", "uncertainty_xy [nm]": "uncertainty_xy", "uncertainty_z [nm]": "uncertainty_z" },
+
+        # Optional
+        "name": "ThunderSTORM (xls)",
+        "description": "a xls format used in thunderSTORM"
+    },
+    "ZEISS (txt)": {
+        # Required
+        "type": "table",
+        "extension": ".txt",
+        "mode": "text",
+        "dtype": "float32",
+        "delimiter": "\t",
+        "comments": "",
+        # specify which row is the header, set to -1 if there is no header
+        "header_row": 0,
+        # specify how to transform the headers to the standard header defined in smlm format,
+        "header_transform": { "Position X [nm]": "x", "Position Y [nm]": "y", "Position Z [nm]": "z", "First Frame": "frame" },
+
+        # Optional
+        "name": "ZEISS (txt)",
+        "description": "a txt format used in ZEISS microscope"
+    },
+    "ZEISSv1 (csv)": {
+        # Required
+        "type": "table",
+        "extension": ".csv",
+        "mode": "text",
+        "dtype": "float32",
+        "delimiter": ";",
+        "comments": "",
+        # specify which row is the header, set to -1 if there is no header
+        "header_row": 0,
+        # specify how to transform the headers to the standard header defined in smlm format,
+        "header_transform": { "Position X [nm]": "x", "Position Y [nm]": "y", "Position Z [nm]": "z", "First Frame": "frame" },
+
+        # Optional
+        "name": "ZEISSv1 (csv)",
+        "description": "a csv format used in ZEISS microscope"
+    },
+    "ZEISSv2 (csv)": {
+        # Required
+        "type": "table",
+        "extension": ".csv",
+        "mode": "text",
+        "dtype": "float32",
+        "delimiter": ";",
+        "comments": "",
+        # specify which row is the header, set to -1 if there is no header
+        "header_row": 0,
+        # specify how to transform the headers to the standard header defined in smlm format,
+        "header_transform": { "x [nm]": "x", "y [nm]": "y", "z [nm]": "z", "First Frame": "frame" },
+
+        # Optional
+        "name": "ZEISSv2 (csv)",
+        "description": "a csv format used for ZEISS microscope"
+    },
+    "RapidSTORM (txt)": {
+        # Required
+        "type": "table",
+        "extension": ".txt",
+        "mode": "text",
+        "dtype": "float32",
+        "delimiter": " ",
+        "comments": "",
+        # specify which row is the header, set to -1 if there is no header
+        "header_row": 0,
+
+        # specify how to transform the headers to the standard header defined in smlm format,
+        "header_transform": { "*all*": 'identifier="([\\w\\d\\-_]+)"', "Position-0-0": "x", "Position-1-0": "y", "Position-2-0": "z", "ImageNumber-0-0": "frame" },
+
+        # Optional
+        "name": "RapidSTORM (txt)",
+        "description": "a text format used in RapidSTORM"
+    },
+    "Space Seperated List (txt)": {
+        # Required
+        "type": "table",
+        "extension": ".txt",
+        "mode": "text",
+        "dtype": "float32",
+        "delimiter": " ",
+        "comments": "",
+        # specify which row is the header, set to -1 if there is no header
+        "header_row": 0,
+
+        # specify how to transform the headers to the standard header defined in smlm format,
+        "header_transform": {},
+
+        # Optional
+        "name": "Space Seperated List (txt)",
+        "description": "A list of coordinates seperated with space."
+    },
+    "Nikon NSTORM (txt)": {
+        # Required
+        "type": "table",
+        "extension": ".txt",
+        "mode": "text",
+        "dtype": "float32",
+        "delimiter": "\t",
+        "comments": "",
+        # specify which row is the header, set to -1 if there is no header
+        "header_row": 0,
+        # specify how to transform the headers to the standard header defined in smlm format,
+        "header_transform": { "X": "x", "Y": "y", "Z": "z", "Frame": "frame" },
+
+        # Optional
+        "name": "Nikon NSTORM (txt)",
+        "description": "a txt format exported from Nikon NSTORM software"
+    },
+}