before photonics west

CHANGELOG.md

@@ -1,6 +1,38 @@
 
 SanPy Documentation is available at [https://cudmore.github.io/SanPy/](https://cudmore.github.io/SanPy/)
 
+## 20240126
+
+ - Added a file folder opening window. This is show at first run and allows users to open new and previous opened files and folder.
+ - Limiting analysis to the visible part of the recording
+ - Greatly improved panning and zooming of all raw data
+   - Retained click+drag to pan x-axis and mouse-wheel to zoom x-axis
+   - New feature using keyboard shift, to click+drag the y-axis and mouse wheel to zoom the y-axis.
+
+- Detailed fixes and additions
+  - Fix a bug where when user sets sweep, we loose the current zoom
+  - Roll over SanPy.log so it does not get too big
+  - fixed spin boxes in plot recording
+  - Fixed bug where `unknown` recording mode was not allowing data to be displayed (problem in initializing the filtered recording).
+  - Now include build date and time on each pi install
+
+ - Known bugs
+  - (seems to be fixed) If user open a plugin and closes the main raw data file, SanPy crashes
+
+### Next release to do
+
+ - Add documentation for Plot Tool plugins
+
+## 20240117
+
+### New features
+ - Now provide opening of one raw data file. Either menu `File - Open` or drag and drop
+ - Add horizontal and vertical cursors to Vm and deriv plot. Can do lots with these including selecting spikes within the cursors and seet some detection params like dv/dt and mV spike threshold as well as some windows like refactory period and window to detect half-widths
+
+### bug fixes
+ - Fixed lots of bugs (and extended the interface) of the plot recording plugin.
+ - Fixed lots of bugs in plotting with `Plot Tool` and `Plot Tool (pool)` plugins.
+
 ## 20231201
 
 ### New Features

docs/docs/download.md

@@ -10,8 +10,8 @@ If you have an older Mac with an Intel/x86 chip then download the **`x86`** vers
 
 If your not sure which type of Mac you have, then download the **`x86`** version.
 
-[Download macOS x86 zip](https://github.com/cudmore/SanPy/releases/download/v0.2.3/SanPy-macOS-x86.zip){ .md-button .md-button--primary}
-[Download macOS arm zip](https://github.com/cudmore/SanPy/releases/download/v0.2.3/SanPy-macOS-arm.zip){ .md-button .md-button--primary}
+[Download macOS x86 zip](https://github.com/cudmore/SanPy/releases/download/v0.2.4/SanPy-macOS-x86.zip){ .md-button .md-button--primary}
+[Download macOS arm zip](https://github.com/cudmore/SanPy/releases/download/v0.2.4/SanPy-macOS-arm.zip){ .md-button .md-button--primary}
 
 ### Mac download and run recipe
 
@@ -24,20 +24,20 @@ If your not sure which type of Mac you have, then download the **`x86`** version
 
 ## Windows download
 
-[Download Windows exe](https://github.com/cudmore/SanPy/releases/download/v0.2.3/SanPy.exe
-){ .md-button .md-button--primary}
+[Download Windows exe](https://github.com/cudmore/SanPy/releases/download/v0.2.4/SanPyWindowsExe.zip){ .md-button .md-button--primary}
 
 ### Windows download and run recipe
 
- - Download the `exe` file
+ - Download the `zip` file
+ - Uncompress the zip file to `SanPy.exe`
  - Once downloaded, double-click on `SanPy.exe` to run SanPy
 
 **Troubleshooting:** If you run into security issues, please see [Security on Windows](#security-on-windows).
 
-<!--
+
 ## Current Version
- - Version 0.1.25, Released on May 12, 2023
--->
+ - Version v0.2.4, Released on Jan 17, 2024
+
 
 ## Current and previous releases (on GitHub)
 

sanpy/analysisDir.py

@@ -4,7 +4,6 @@
 
 import os
 import time
-import sys
 import copy  # For copy.deepcopy() of bAnalysis
 # import uuid  # to generate unique key on bAnalysis spike detect
 import pathlib  # ned to use this (introduced in Python 3.4) to maname paths on Windows, stop using os.path
@@ -468,8 +467,7 @@ class analysisDir:
 
     def __init__(
         self,
-        path: str = None,
-        filePath : str = None,
+        path : str = None,
         sanPyWindow : "sanpy.interface.SanPyWindow" = None,
         fileLoaderDict : dict = None,
         autoLoad: bool = False,
@@ -484,9 +482,7 @@ def __init__(
         Parameters
         ----------
         path (str):
-            Path to folder
-        filePath (str):
-            Path to one file
+            Path to file or folder
         sanPyWindow (sanpy.interface.SanPyWindow)
             PyQt, used to signal progress on loading
         fileLoaderDict (dict):
@@ -503,14 +499,16 @@ def __init__(
         - 202312 adding filepath to load just one file
         """
 
-        self._filePath = filePath
-        if filePath is not None and os.path.isfile(filePath):
-            self._filePath = filePath
-            path = os.path.split(filePath)[0]
+        self._filePath = None
+        if os.path.isfile(path):
+            self._filePath = path
+            folderPath = os.path.split(path)[0]
+        else:
+            folderPath = path
 
-        logger.info(f'{path} self._filePath:{self._filePath}')
+        logger.info(f'{path}')
 
-        self.path: str = path
+        self.path: str = folderPath  # path to folder
 
         self._sanPyWindow = sanPyWindow
         # used to signal on building initial db
@@ -548,10 +546,10 @@ def __init__(
             self.syncDfWithPath()
 
         # if we have a filePath and not in df then add it
-        if self._filePath is not None:
+        # if self._filePath is not None:
 
-            logger.info('self._df')
-            print(self._df)
+        #     logger.info('self._df')
+        #     print(self._df)
 
         # self._df = self.loadFolder(loadData=autoLoad)
 
@@ -970,13 +968,13 @@ def loadFolder(self, path=None, loadData=False) -> pd.DataFrame:
 
         return df
 
-    def _checkColumns(self):
+    def _checkColumns(self, verbose = False):
         """Check columns in loaded vs sanpyColumns (and vica versa).
         """
         if self._df is None:
             return
 
-        verbose = True
+        # verbose = True
         loadedColumns = self._df.columns
         for col in loadedColumns:
             if col not in self.sanpyColumns.keys():
@@ -986,11 +984,12 @@ def _checkColumns(self):
                         f'did not find loaded col: "{col}" in sanpyColumns.keys() ... ignore it'
                     )
         for col in self.sanpyColumns.keys():
-            if not col in loadedColumns:
+            if col not in loadedColumns:
                 # loaded is missing expected, add it
-                logger.info(
-                    f'did not find sanpyColumns.keys() col: "{col}" in loadedColumns ... adding col'
-                )
+                if verbose:
+                    logger.info(
+                        f'did not find sanpyColumns.keys() col: "{col}" in loadedColumns ... adding col'
+                    )
                 self._df[col] = ""
 
     def _updateLoadedAnalyzed(self, theRowIdx=None):
@@ -1225,8 +1224,8 @@ def _setColumnType(self, df):
         # print('columns are:', df.columns)
         for col in df.columns:
             # when loading from csv, 'col' may not be in sanpyColumns
-            if not col in self.sanpyColumns:
-                logger.warning(f'Column "{col}" is not in sanpyColumns -->> ignoring')
+            if col not in self.sanpyColumns:
+                # logger.warning(f'Column "{col}" is not in sanpyColumns -->> ignoring')
                 continue
             colType = self.sanpyColumns[col]["type"]
             # print(f'  _setColumnType() for "{col}" is type "{colType}"')
@@ -1501,10 +1500,10 @@ def appendRow(self, rowDict=None, ba=None):
         # logger.warning(f"need to replace append with concat")
         #df = df.append(rowSeries, ignore_index=True)
 
-        logger.info('concat this rowSeries')
-        print(rowSeries)
-        print('to this df')
-        print(df)
+        # logger.info('concat this rowSeries')
+        # print(rowSeries)
+        # print('to this df')
+        # print(df)
 
         df = pd.concat([df, rowSeries], axis=0, ignore_index=True)
 
@@ -1514,9 +1513,9 @@ def appendRow(self, rowDict=None, ba=None):
         if ba is not None:
             df.loc[newRowIdx, "_ba"] = ba
 
-        print('')
-        logger.info('=== after concat')
-        print(df)
+        # print('')
+        # logger.info('=== after concat')
+        # print(df)
 
         #
         self._df = df

sanpy/bAnalysis_.py

@@ -855,17 +855,20 @@ def _rebuildFiltered(self):
             logger.warning("not getting derivative ... sweepX was none?")
             return
 
-        if (
-            self.fileLoader.recordingMode == recordingModes.iclamp
-            or self.fileLoader.recordingMode == recordingModes.kymograph
-        ):
-            self.fileLoader._getDerivative()
-        elif self.fileLoader.recordingMode == recordingModes.vclamp:
-            self.fileLoader._getDerivative()
-        else:
-            logger.warning(
-                f'Did not take derivative, unknown recording mode "{self.fileLoader.recordingMode}"'
-            )
+        self.fileLoader._getDerivative()
+
+        # if (
+        #     self.fileLoader.recordingMode == recordingModes.iclamp
+        #     or self.fileLoader.recordingMode == recordingModes.kymograph
+        # ):
+        #     self.fileLoader._getDerivative()
+        # elif self.fileLoader.recordingMode == recordingModes.vclamp:
+        #     self.fileLoader._getDerivative()
+        # else:
+        #     logger.warning(
+        #         f'Did not take derivative, unknown recording mode "{self.fileLoader.recordingMode}"'
+        #     )
+        #     self.fileLoader._getDerivative()
 
     def _getFilteredRecording(self):
         """

sanpy/fileloaders/epochTable.py

@@ -60,7 +60,7 @@ def getSweepEpoch(self, sweep):
         return self._epochList[sweep]
 
     def _builFromAbf(self, abf: pyabf.ABF):
-        dataPointsPerMs = abf.dataPointsPerMs
+        # dataPointsPerMs = abf.dataPointsPerMs
         """To convert point to seconds"""
 
         try:
@@ -69,18 +69,30 @@ def _builFromAbf(self, abf: pyabf.ABF):
             logger.error(e)
             return
 
+        # abf.sweepEpoch is
+        # pyabf.waveform.EpochSweepWaveform
+        # logger.info(f'   abf.sweepEpochs is {type(abf.sweepEpochs)}')
+        # print(abf.sweepEpochs)
+
+        # print(pyabf.waveform.epochTable())
+
         # sweepEpochs is type "pyabf.waveform.EpochSweepWaveform"
         for epochIdx, p1 in enumerate(abf.sweepEpochs.p1s):
             p2 = abf.sweepEpochs.p2s[epochIdx]  # stop point of each pulse
             epochLevel = abf.sweepEpochs.levels[epochIdx]
             epochType = abf.sweepEpochs.types[epochIdx]
             pulseWidth = abf.sweepEpochs.pulseWidths[epochIdx]
             pulsePeriod = abf.sweepEpochs.pulsePeriods[epochIdx]
-            digitalState = abf.sweepEpochs.pulsePeriods[epochIdx]
+            digitalState = abf.sweepEpochs.digitalStates[epochIdx]  # 20240117 owl-analysis
             ##print(f"epoch index {epochIdx}: at point {p1} there is a {epochType} to level {epochLevel}")
 
-            p1_sec = p1 / abf.dataPointsPerMs / 1000
-            p2_sec = p2 / abf.dataPointsPerMs / 1000
+            try:
+                p1_sec = p1 / abf.dataPointsPerMs / 1000
+                p2_sec = p2 / abf.dataPointsPerMs / 1000
+            except (ZeroDivisionError) as e:
+                logger.error(f'ZeroDivisionError: {e}')
+                p1_sec = float('nan')
+                p2_sec = float('nan')
 
             epochDict = {
                 "sweepNumber": abf.sweepNumber,
@@ -160,19 +172,39 @@ def numEpochs(self):
 
 
 if __name__ == "__main__":
+    import matplotlib.pyplot as plt
     import sanpy
 
     # path = '/Users/cudmore/Sites/SanPy/data/19114000.abf'
     path = "/Users/cudmore/data/theanne-griffith/07.28.21/2021_07_28_0001.abf"
 
+    path = '/Users/cudmore/Dropbox/data/sanpy-users/porter/data/2022_08_15_0022.abf'
+
     ba = sanpy.bAnalysis(path)
     print(ba)
 
-    sweep = 13
-
-    et = ba.fileLoader.getEpochTable(sweep)
-    df = et.getEpochList(asDataFrame=True)
-    pprint(df)
+    _abf = pyabf.ABF(path)
+    # _epochTable = pyabf.waveform.EpochTable(_abf, 1)
+    # print('   _epochTable')
+    # print(_epochTable)
+
+    sweeps = [9, 10, 11]
+    for sweep in sweeps:
+        ba.setSweep(sweep)
+        et = ba.fileLoader.getEpochTable(sweep)
+        df = et.getEpochList(asDataFrame=True)
+        print(f'   sweep:{sweep}')
+        pprint(df)
+
+        # owl
+        #<bound method ABF.sweepD of ABF (v2.9) with 1 channel (pA), sampled at 10.0 kHz, containing 18 sweeps, having no tags, with a total length of 6.33 minutes, recorded with protocol "PPR_v-clamp_owl". path=/Users/cudmore/Dropbox/data/sanpy-users/porter/2022_08_15_0022.abf>
+        # print('self._abf.sweepD')
+        # for _i in range(8):
+        #     print(_i)
+        #     print(self._abf.sweepD(_i))
+        _abf.setSweep(sweep)
+        for _i in range(8):
+            _sweepD = _abf.sweepD(_i)
 
     testPnt = 1280
     epochIndex = et.findEpoch(testPnt)

sanpy/fileloaders/fileLoader_abf.py

@@ -77,6 +77,15 @@ def _loadAbf(
 
             # on load, sweep is 0
             if loadData:
+
+                # owl
+                #<bound method ABF.sweepD of ABF (v2.9) with 1 channel (pA), sampled at 10.0 kHz, containing 18 sweeps, having no tags, with a total length of 6.33 minutes, recorded with protocol "PPR_v-clamp_owl". path=/Users/cudmore/Dropbox/data/sanpy-users/porter/2022_08_15_0022.abf>
+                # print('self._abf.sweepD')
+                # for _i in range(8):
+                #     print(_i)
+                #     print(self._abf.sweepD(_i))
+
+
                 _numRows = self._abf.sweepX.shape[0]
                 numSweeps = len(self._sweepList)
                 self._sweepX = np.zeros((_numRows, 1))
@@ -118,8 +127,10 @@ def _loadAbf(
 
             acqDate = abfDateTime.strftime("%Y-%m-%d")
             acqTime = abfDateTime.strftime("%H:%M:%S")
-            logger.info(f'acqDate:"{acqDate}')
-            logger.info(f'acqTime:"{acqTime}')
+
+            # logger.info(f'acqDate:"{acqDate}')
+            # logger.info(f'acqTime:"{acqTime}')
+
             # self._acqDate = abfDateTime.strftime("%Y-%m-%d")
             # self._acqTime = abfDateTime.strftime("%H:%M:%S")
 
@@ -143,15 +154,20 @@ def _loadAbf(
 
             # self._sweepLabelX = self._abf.sweepLabelX
             # self._sweepLabelY = self._abf.sweepLabelY
-            if self._sweepLabelY in ["pA", "nA"]:
+            if self._sweepLabelY in ["A", "pA", "nA", "uA"]:
                 self._recordingMode = recordingModes.vclamp  # 'V-Clamp'
                 # self._sweepY_label = self._abf.sweepUnitsY
-            elif self._sweepLabelY in ["mV"]:
+            elif self._sweepLabelY in ["mV", "uv", "V"]:
                 self._recordingMode = recordingModes.iclamp  #'I-Clamp'
                 # self._sweepY_label = self._abf.sweepUnitsY
             else:
                 logger.warning(f'did not understand adcUnit "{adcUnits}"')
 
+            # 20240125 ownanalysis
+            self._userList = self._abf.userList
+            if self._userList is not None:
+                logger.info(f'_userList:{self._userList}')
+
         #
         self.myFileType = "abf"