making single file script for a better approach

Author: scivision

README.md

@@ -67,5 +67,5 @@ These examples are old, now we use HDF5 files. Kept for reference only.
 
 ```sh
 from histutils import rawDMCreader
-data = rawDMCreader.goRead('myfile.DMCdata')[0]
+data = rawDMCreader.read('myfile.DMCdata')[0]
 ```

examples/Convert2013-04-11.py

@@ -0,0 +1,25 @@
+#!/usr/bin/env python3
+"""
+Convert raw DMCdata from 2013-04-11 to HDF5
+"""
+
+import histutils.dio
+import histutils.rawDMCreader
+
+# path to the data. This will probably be distinct for your computer.
+fn = "~/Google Drive/My Drive/Data/PokerFlat/2013-04-11/hst/raw/2013-04-11T07-00-CamSer1387_frames_402209-1-403708.DMCdata"
+
+# where to store the converted data
+outdir = "./"
+
+# TODO: these should be read from XML file.
+
+params = {
+    "header_bytes": 4,  # only 2011-era files have 0 header bytes.
+    "xy_pixel": (512, 512),  # usually, but some files are 256x256.
+    "xy_bin": (1, 1),  # usually, but some files are binned 2x2.
+          }
+
+_, rawind, finf = histutils.rawDMCreader.read(fn, params)
+
+histutils.dio.vid2h5(None, ut1=finf["ut1"], rawind=rawind, ticks=None, params=params)

src/histutils/convert/__main__.py

@@ -26,10 +26,13 @@
 
 #
 from ..dio import dir2fn, vid2h5
-from ..rawDMCreader import goRead
+from ..rawDMCreader import read
 
 
-def dmclooper(p: dict):
+def convert_files(p: dict):
+    """
+    converts .DMCdata files to .h5 files, with metadata
+    """
 
     params = {
         "kineticsec": p["kineticsec"],
@@ -67,7 +70,7 @@ def dmclooper(p: dict):
             f"\n file {i + 1} / {N}   {i + 1 / N * 100.0:.1f} % done with {flist[0].parent}"
         )
 
-        rawImgData, rawind, finf = goRead(fn, params)
+        rawImgData, rawind, finf = read(fn, params)
         # %% convert
         vid2h5(None, ut1=finf["ut1"], rawind=rawind, ticks=None, params=params)
 
@@ -152,4 +155,4 @@ def dmclooper(p: dict):
         level=logging.INFO,
     )
 
-    dmclooper(vars(P))
+    convert_files(vars(P))

src/histutils/index.py

@@ -5,6 +5,10 @@
 
 
 def getRawInd(fn: Path, finf: dict[str, int]) -> tuple[int, int]:
+
+    if not fn.is_file():
+        raise FileNotFoundError(fn)
+
     if not isinstance(finf["nmetadata"], int):
         raise TypeError(finf["nmetadata"])
 

src/histutils/rawDMCreader.py

@@ -21,12 +21,12 @@
 # NHEADBYTES = 4
 
 
-def goRead(infn: Path, params: dict[str, T.Any]) -> tuple:
+def read(infn: str | Path, params: dict[str, T.Any]) -> tuple:
 
-    infn = Path(infn).expanduser()
+    fn = Path(infn).expanduser()
     # %% setup data parameters
     # preallocate *** LABVIEW USES ROW-MAJOR ORDERING C ORDER
-    finf = getDMCparam(infn, params)
+    finf = getDMCparam(fn, params)
     write_quota(finf["bytes_frame"] * finf["nframeextract"], params.get("outfn"))
 
     rawFrameInd = np.zeros(finf["nframeextract"], dtype=np.int64)
@@ -41,7 +41,7 @@ def goRead(infn: Path, params: dict[str, T.Any]) -> tuple:
             order="C",
         )
     # %% read
-    with infn.open("rb") as fid:
+    with fn.open("rb") as fid:
         # j and i are NOT the same in general when not starting from beginning of file!
         for j, i in enumerate(finf["frameindrel"]):
             D, rawFrameInd[j] = getDMCframe(fid, i, finf)
@@ -67,9 +67,6 @@ def getDMCparam(fn: Path, params: dict[str, T.Any]) -> dict[str, T.Any]:
         "header_bytes": params["header_bytes"],
     }  # FIXME for DMCdata version 1 only
 
-    if not fn.is_file():  # leave this here, getsize() doesn't fail on directory
-        raise FileNotFoundError(fn)
-
     # int() in case we are fed a float or int
     finf["super_x"] = int(params["xy_pixel"][0] // params["xy_bin"][0])
     finf["super_y"] = int(params["xy_pixel"][1] // params["xy_bin"][1])
@@ -97,6 +94,9 @@ def howbig(params: dict[str, T.Any], finf: dict[str, T.Any]) -> dict[str, int]:
 
 def whichframes(fn: Path, params: dict[str, T.Any], finf: dict[str, T.Any]):
 
+    if not fn.is_file():
+        raise FileNotFoundError(fn)
+
     fileSizeBytes = fn.stat().st_size
 
     if fileSizeBytes < finf["bytes_image"]:

src/histutils/tests/test_all.py

@@ -2,7 +2,7 @@
 from pathlib import Path
 import numpy as np
 
-from histutils.rawDMCreader import goRead
+from histutils.rawDMCreader import read
 
 R = Path(__file__).parent
 
@@ -17,9 +17,9 @@ def test_rawread():
         "header_bytes": 4,
     }
 
-    testframe, testind, finf = goRead(bigfn, params)
+    testframe, testind, finf = read(bigfn, params)
 
-    # these are both tested by goRead
+    # these are both tested by read
     # finf = getDMCparam(bigfn,(512,512),(1,1),None,verbose=2)
     # with open(bigfn,'rb') as f:
     #    testframe,testind = getDMCframe(f,iFrm=1,finf=finf,verbose=2)