fixed the bug in load_openpiv_txt

examples/notebooks/test_reading_different_files.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -11,101 +11,82 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
     "import xarray as xr\n",
     "from typing import List \n",
     "import numpy as np\n",
     "import pandas as pd\n",
-    "import pkg_resources as pkg\n"
+    "import pkg_resources as pkg\n",
+    "import matplotlib.pyplot as plt\n",
+    "%matplotlib inline\n"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "[PosixPath('/home/user/Documents/repos/pivpy/pivpy/data/Insight'), PosixPath('/home/user/Documents/repos/pivpy/pivpy/data/PIV_Challenge'), PosixPath('/home/user/Documents/repos/pivpy/pivpy/data/day2'), PosixPath('/home/user/Documents/repos/pivpy/pivpy/data/openpiv'), PosixPath('/home/user/Documents/repos/pivpy/pivpy/data/urban_canopy')]\n",
-      "/home/user/Documents/repos/pivpy/pivpy/data/Insight/Run000001.T000.D000.P000.H001.L.vec\n",
-      "/home/user/Documents/repos/pivpy/pivpy/data/PIV_Challenge/B00001.txt\n",
-      "/home/user/Documents/repos/pivpy/pivpy/data/day2/day2a005000.T000.D000.P003.H001.L.vec\n",
-      "/home/user/Documents/repos/pivpy/pivpy/data/openpiv/exp1_001_b.txt\n",
-      "/home/user/Documents/repos/pivpy/pivpy/data/urban_canopy/B00001.vc7\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "import pathlib\n",
     "\n",
     "path = pathlib.Path(pkg.resource_filename(\"pivpy\", \"data\"))\n",
     "subdirs = [x for x in sorted(path.glob('**/*')) if x.is_dir()]\n",
-    "# subdirs = [s for s in subdirs if s.stem != '.ipynb_checkpoints']\n",
-    "print(subdirs)\n",
+    "subdirs = [s for s in subdirs if s.stem != '.ipynb_checkpoints']\n",
     "\n",
-    "# sorted(dirs[0].rglob('[!.]*'))\n",
     "test_files = []\n",
     "for d in subdirs:\n",
-    "    files = [x for x in sorted(d.rglob('[!.]*')) if not x.is_dir() ]\n",
-    "    print(files[0])\n",
-    "    test_files.append(files[0])"
+    "    files = [x for x in sorted(d.glob('[!.]*')) if not x.is_dir() ]\n",
+    "    test_files.append(files[0])\n",
+    "    \n",
+    "print(test_files)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "/home/user/Documents/repos/pivpy/pivpy/data/Insight/Run000001.T000.D000.P000.H001.L.vec\n",
-      "Run000001.T000.D000.P000.H001.L\n",
-      "1\n",
-      "/home/user/Documents/repos/pivpy/pivpy/data/PIV_Challenge/B00001.txt\n",
-      "B00001\n",
-      "1\n",
-      "/home/user/Documents/repos/pivpy/pivpy/data/day2/day2a005000.T000.D000.P003.H001.L.vec\n",
-      "day2a005000.T000.D000.P003.H001.L\n",
-      "5000\n",
-      "/home/user/Documents/repos/pivpy/pivpy/data/openpiv/exp1_001_b.txt\n",
-      "exp1_001_b\n",
-      "1\n",
-      "/home/user/Documents/repos/pivpy/pivpy/data/urban_canopy/B00001.vc7\n",
-      "B00001\n",
-      "1\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "from pivpy.io import *\n",
     "\n",
     "for file in test_files:\n",
-    "    print(file)\n",
-    "    print(file.stem)\n",
+    "     #print(file)\n",
+    "    # print(file.stem)\n",
     "    variables, units, rows, cols, dt, frame, method = parse_header(file)\n",
-    "    print(frame)\n",
+    "    # print(f'frame = {frame}')\n",
+    "    print(file.stem, method)\n",
     "    ds = method(file)\n",
-    "    # print(ds.head())\n"
+    "    plt.figure()\n",
+    "    ds.isel(t=0).piv.quiver(arrScale=5)\n",
+    "    plt.title(file.stem)\n",
+    "    \n",
+    "    \n",
+    "    if file.suffix == '.vec':\n",
+    "        try:\n",
+    "            # try another method\n",
+    "            ds = load_insight_vec_as_csv(file)\n",
+    "            plt.figure()\n",
+    "            ds.isel(t=0).piv.quiver(arrScale=5)\n",
+    "            plt.title(file.stem)\n",
+    "        except:\n",
+    "            pass\n",
+    "    elif file.suffix == '.txt':\n",
+    "        try:\n",
+    "            ds  = load_openpiv_txt_as_csv(file)\n",
+    "            plt.figure()\n",
+    "            ds.isel(t=0).piv.quiver(arrScale=5)\n",
+    "            plt.title(file.stem)\n",
+    "        except:\n",
+    "            pass\n"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3.8.12 64-bit",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -121,13 +102,12 @@
    "pygments_lexer": "ipython3",
    "version": "3.8.12"
   },
-  "orig_nbformat": 4,
   "vscode": {
    "interpreter": {
     "hash": "cc9f4a0bb10ffa66460a048df631f1f9f016c2b1c927bb3119f96382f3a023b9"
    }
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }

pivpy/io.py

@@ -214,14 +214,14 @@ def from_df(
 
     x, ix = unsorted_unique(d[:, 0])
     y, iy = unsorted_unique(d[:, 1])
-    if d.shape[1] < 5:  # not always there's a mask
-        tmp = np.ones((d.shape[0], 5))
-        tmp[:, :-1] = d
-        d = tmp
+
+    if d.shape[1] < 5: # davis8 does not have mask or chc
+        d = np.column_stack((d,np.zeros_like(d[:,-1])))
+
     if ix[1] == 1: #x grows first
         d = d.reshape(len(y), len(x), 5).transpose(1, 0, 2)
     elif iy[1] == 1: # y grows first
-        d = d.reshape(len(y), len(x), 5) # .transpose(1,0,2)
+        d = d.reshape(len(x), len(y), 5) # .transpose(1,0,2)
     else:
         raise ValueError('not sorted x or y')
 
@@ -269,26 +269,33 @@ def load_vec(
     """
     if rows is None or cols is None:
         _, _, rows, cols, dt, frame, _ = parse_header(filename)
+        # print(f'rows = {rows}, cols = {cols}')
 
-    if rows is None:  # means no headers
-        d = np.genfromtxt(filename, usecols=(0, 1, 2, 3, 4))
+    if rows is None:  # means no headers, openpiv vec file
+        # d = np.genfromtxt(filename, usecols=(0, 1, 2, 3, 4))
+        d = np.genfromtxt(
+            filename, 
+            usecols=(0, 1, 2, 3, 4)
+          )
         x, ix = unsorted_unique(d[:, 0])
         y, iy = unsorted_unique(d[:, 1])
+
+        # print(f'rows = {len(y)}, cols = {len(x)}')
+
         if ix[1] == 1: #x grows first
             d = d.reshape(len(y), len(x), 5).transpose(1, 0, 2)
         elif iy[1] == 1: # y grows first
             d = d.reshape(len(y), len(x), 5) # .transpose(1,0,2)
         else:
             raise ValueError('not sorted x or y')
-    else:
-        # d = np.genfromtxt(
-        #     filename, skiprows=1, delimiter=",", usecols=(0, 1, 2, 3, 4)
-        # ).reshape(rows, cols, 5)
+    else: # Insight VEC file
         d = np.genfromtxt(
             filename, skip_header=1, delimiter=",", usecols=(0, 1, 2, 3, 4)
-        ).reshape(cols, rows, 5)
-        x = d[:, :, 0][0, :]
-        y = d[:, :, 1][:, 0]
+        ).reshape(cols, rows, 5).transpose(1, 0, 2)
+
+        x = d[:, :, 0][:, 0]
+        y = d[:, :, 1][0, :]
+
 
     u = d[:, :, 2]
     v = d[:, :, 3]
@@ -313,6 +320,33 @@ def load_vec(
 
     return dataset
 
+def load_insight_vec_as_csv(
+    filename: pathlib.Path,
+    rows: int = None,
+    cols: int = None,
+    delta_t: float = None,
+    frame: int = 0,
+) -> xr.Dataset:
+    """
+    load_insight_vec_as_csv(filename,rows=rows,cols=cols)
+    Loads the VEC file (TECPLOT format by TSI Inc.),
+    Arguments:
+        filename : file name, expected to have a header and 5 columns
+        rows, cols : number of rows and columns of a vector field,
+        if None, None, then parse_header is called to infer the number
+        written in the header
+        DELTA_T : time interval (default is None)
+        frame : frame or time marker (default is None)
+    Output:
+        dataset is a xAarray Dataset, see xarray for help
+    """    
+    df = pd.read_csv(filename,header=None,skiprows=1,names=["x","y","u","v","chc"])
+    dataset = from_df(df,frame=frame,filename=filename)
+
+    return dataset
+
+
+
 
 def load_vc7(
     filename: pathlib.Path,
@@ -596,6 +630,45 @@ def load_openpiv_txt(
     return dataset
 
 
+def load_openpiv_txt_as_csv(
+    filename: str,
+    rows: int = None,
+    cols: int = None,
+    delta_t: float = None,
+    frame: int = 0,
+) -> xr.Dataset:
+    """ loads OpenPIV txt file 
+
+    Args:
+        filename (str): _description_
+        rows (int, optional): _description_. Defaults to None.
+        cols (int, optional): _description_. Defaults to None.
+        delta_t (float, optional): _description_. Defaults to None.
+        frame (int, optional): _description_. Defaults to 0.
+
+    Returns:
+        xr.Dataset: _description_
+    """
+    df = pd.read_csv(
+        filename, 
+        header=None,
+        names=['x','y','u','v','chc'],
+        delim_whitespace=True
+    )
+
+    dataset = from_df(
+        df,
+        frame=frame,
+        filename=filename
+    )
+
+    return dataset
+
+
+
+
+
+
 def load_davis8_txt(
     filename: pathlib.Path,
     rows: int = None, # pylint: disable=W0613
@@ -618,7 +691,7 @@ def load_davis8_txt(
     dataframe = pd.read_csv(
         filename, delimiter="\t", skiprows=1, names=["x", "y", "u", "v"], decimal=","
     )
-    dataset = from_df(dataframe, frame=frame)
+    dataset = from_df(dataframe, frame=frame,filename=filename)
     # print(f'{rows},{cols},{delta_t}')
     return dataset
 

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "pivpy"
-version = "0.0.17"
+version = "0.0.18"
 authors = [
   { name="Alex Liberzon and Ron Shnapp", email="[email protected]" },
 ]

tests/test_graphics.py

@@ -40,7 +40,8 @@ def test_histogram():
 def test_quiver_openpiv_vec():
     """ tests quiver of openpiv vec file
     """
-    filename = pathlib.Path(pkg.resource_filename("pivpy", "data")) / "openpiv" / "exp1_001_b.vec"
+    filename = pathlib.Path(
+        pkg.resource_filename("pivpy", "data")) / "openpiv_vec" / "exp1_001_b.vec"
     print(filename, filename.exists())
     _d = io.load_vec(filename)
     _d.piv.quiver() # notice the warning

tests/test_io.py

@@ -7,7 +7,7 @@
 path = pathlib.Path(pkg.resource_filename("pivpy", "data"))
 
 vec_file = path / "Insight" / "Run000002.T000.D000.P000.H001.L.vec" 
-openpiv_txt_file = path / "openpiv" / "exp1_001_b.txt"
+openpiv_txt_file = path / "openpiv_txt" / "exp1_001_b.txt"
 
 
 def test_get_dt():
@@ -27,11 +27,11 @@ def test_get_frame():
     )
     assert frame == 2
     _, _, _, _, _, frame,_ = io.parse_header(
-        path / "openpiv" / "exp1_001_b.vec"
+        path / "openpiv_vec" / "exp1_001_b.vec"
         )
     assert frame == 1
     _, _, _, _, _, frame,_ = io.parse_header(
-        path / "openpiv" / "exp1_001_b.txt"
+        path / "openpiv_txt" / "exp1_001_b.txt"
     )
     assert frame == 1