Merge pull request #129 from lucarossi147/main

ABF loading optimization and improved support for variable-length sweeps
swharden · Sep 27, 2022 · aa79309 · aa79309
2 parents 81d011d + be6121c
commit aa79309
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Showing 7 changed files with 22 additions and 18 deletions.
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -7,18 +7,21 @@ on:
 
 jobs:
   test:
-    name: Test on ${{ matrix.os }}
+    name: Test Python ${{ matrix.python-version }} on ${{ matrix.os }}
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-
+        python-version: ["3.7", "3.x"]
+
     runs-on: ${{ matrix.os }}
     steps:
       - name: 🛒 Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: 🐍 Get Python
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
 
       - name: 🚚 Get Dependencies
         run: |

diff --git a/.github/workflows/package.yaml b/.github/workflows/package.yaml
@@ -9,10 +9,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: 🛒 Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: 🐍 Get Python
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
 
       - name: 🛠️ Setup Build
         run: python -m pip install build --user

diff --git a/.github/workflows/website.yaml b/.github/workflows/website.yaml
@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: 🛒 Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: ✨ Setup Hugo
         env:

diff --git a/src/pyabf/__init__.py b/src/pyabf/__init__.py
@@ -5,7 +5,7 @@
 Documentation and code examples, and more can be found at:
     https://github.com/swharden/pyABF
 """
-__version__ = '2.3.6'
+__version__ = '2.3.7'
 
 import sys
 import os

diff --git a/src/pyabf/abf.py b/src/pyabf/abf.py
@@ -472,8 +472,7 @@ def _loadAndScaleData(self, fb: BufferedReader):
         nRows = self.channelCount
         nCols = int(self.dataPointCount/self.channelCount)
         raw = np.reshape(raw, (nCols, nRows))
-        raw = np.rot90(raw)
-        raw = raw[::-1]
+        raw = np.transpose(raw)
 
         # if data is int, scale it to float32 so we can scale it
         self.data = raw.astype(np.float32)
@@ -642,9 +641,9 @@ def setSweep(self,
             pointCount = self.sweepPointCount
         else:
             pointStart = 0
-            for i in range(1, sweepNumber):
-                pointStart += self._synchArraySection.lLength[i-1]
-            pointCount = self._synchArraySection.lLength[sweepNumber]
+            for i in range(sweepNumber):
+                pointStart += self._synchArraySection.lLength[i]//self.channelCount
+            pointCount = self._synchArraySection.lLength[sweepNumber]//self.channelCount
         pointEnd = pointStart + pointCount
 
         # load the actual sweep data

diff --git a/src/setup.py b/src/setup.py
@@ -14,7 +14,7 @@
 # standard pypi stuff
 setup(
     name='pyabf',
-    version='2.3.6',
+    version='2.3.7',
     author='Scott W Harden',
     author_email='SWHarden@gmail.com',
     python_requires='>=3.6',

diff --git a/tests/test_sweepHashes.py b/tests/test_sweepHashes.py
@@ -1275,11 +1275,11 @@
 knownAbfSweepValues["2020_03_02_0000.abf SW15 CH1"] = "20000, 9.46044922, -0.30517578, 259.74499512"
 
 knownAbfSweepValues["2020_06_16_0000.abf SW0 CH0"] = "3540, 0.91552734, 0.00000000, 0.34947360"
-knownAbfSweepValues["2020_06_16_0000.abf SW1 CH0"] = "70040, 0.91552734, 0.61035156, 0.34824026"
-knownAbfSweepValues["2020_06_16_0000.abf SW2 CH0"] = "16040, -0.30517578, 0.61035156, 0.35196608"
+knownAbfSweepValues["2020_06_16_0000.abf SW1 CH0"] = "70040, -0.30517578, 0.30517578, 0.34824499"
+knownAbfSweepValues["2020_06_16_0000.abf SW2 CH0"] = "16040, 0.61035156, 0.30517578, 0.35050380"
 
 knownAbfSweepValues["2020_06_16_0001.abf SW0 CH0"] = "22040, 0.61035156, 0.00000000, 0.34784842"
-knownAbfSweepValues["2020_06_16_0001.abf SW1 CH0"] = "11040, 0.61035156, 0.61035156, 0.34771526"
+knownAbfSweepValues["2020_06_16_0001.abf SW1 CH0"] = "11040, -0.30517578, 0.91552734, 0.35148475"
 
 knownAbfSweepValues["abf1_with_tags.abf SW0 CH0"] = "18000000, -34.54589462, -80.74950409, 6.65401363"
 
@@ -2659,4 +2659,4 @@
 knownAbfSweepValues["test_0001.abf SW0 CH12"] = "12896, -0.00122070, -0.00122070, 0.00017642"
 knownAbfSweepValues["test_0001.abf SW0 CH13"] = "12896, 0.00152588, 0.00183105, 0.00016845"
 knownAbfSweepValues["test_0001.abf SW0 CH14"] = "12896, -0.21362305, -0.18310547, 0.01735568"
-knownAbfSweepValues["test_0001.abf SW0 CH15"] = "12896, 0.00000000, 0.00000000, 0.00191588"
+knownAbfSweepValues["test_0001.abf SW0 CH15"] = "12896, 0.00000000, 0.00000000, 0.00191588"