Merge pull request #14 from Aharoni-Lab/wireless_fpga

feat: add support for wireless fpga-based manchester daq

.gitignore

@@ -4,7 +4,7 @@ __pycache__/
 *$py.class
 
 # C extensions
-*.so
+# *.so
 
 # Distribution / packaging
 .Python
@@ -14,7 +14,6 @@ dist/
 downloads/
 eggs/
 .eggs/
-lib/
 lib64/
 parts/
 sdist/

README.md

@@ -4,3 +4,13 @@
 Functionality not guaranteed
 -<3 jonny)
 
+
+
+## Licensing
+
+This package includes software sublicensed from more 
+restrictive licenses. Those licenses can be found
+in the `LICENSE` files in the respective directories 
+containing the unmodified source material
+
+* `miniscope_io/vendor/opalkelly`

docs/api/devices.md

@@ -0,0 +1,11 @@
+# Devices
+
+Interfaces to external devices like miniscopes and DAQs
+
+## OpalKelly
+
+```{eval-rst}
+.. autoclass:: miniscope_io.devices.opalkelly.okDev
+    :members:
+    :undoc-members:
+```

docs/api/index.md

@@ -4,10 +4,13 @@
 :caption: API
 
 data
+devices
 formats
 io
 sdcard
 exceptions
 plots/index
 utils
+uart_daq
+vendor/index
 ```

docs/api/uart_daq.md

@@ -0,0 +1,11 @@
+# UART Daq
+
+(Some description of what this module does, can happen either here in markdown
+or in the module docstring as RST)
+
+```{eval-rst}
+.. automodule:: miniscope_io.uart_daq
+    :members:
+    :undoc-members:
+```
+

docs/api/vendor/index.md

@@ -0,0 +1,9 @@
+# Vendor
+
+Modules that incorporate some proprietary/nonfree component and are vendored in
+
+```{toctree}
+:caption: Vendor
+
+opalkelly
+```

docs/api/vendor/opalkelly.md

@@ -0,0 +1,4 @@
+# OpalKelly FrontPanel
+
+(your docs on what this is for and how it works here!!!)
+

docs/conf.py

@@ -20,7 +20,8 @@
     'sphinx.ext.napoleon',
     'sphinx.ext.autodoc',
     'sphinxcontrib.autodoc_pydantic',
-    'sphinx.ext.intersphinx'
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.todo'
 ]
 
 templates_path = ['_templates']
@@ -62,4 +63,13 @@
 napoleon_attr_annotations = True
 
 # graphviz
-graphviz_output_format = "svg"
+graphviz_output_format = "svg"
+
+
+# autodoc
+# Mock imports for packages we don't have yet - this one is
+# for opal kelley stuff we need to figure out the licensing for
+autodoc_mock_imports = ['routine']
+
+# todo
+todo_include_todos = True

docs/guide/index.md

@@ -0,0 +1,5 @@
+# Guide
+
+```{toctree}
+installation
+```

docs/guide/installation.md

@@ -0,0 +1,50 @@
+# Installation
+
+From PyPI:
+
+```bash
+pip install miniscope_io
+```
+
+From git repository, using pip:
+```bash
+git clone https://github.com/Aharoni-Lab/miniscope-io
+cd miniscope-io
+pip install .
+```
+
+Or poetry:
+```bash
+git clone https://github.com/Aharoni-Lab/miniscope-io
+cd miniscope-io
+poetry install
+```
+
+
+## Additional Dependencies
+
+### OpalKelly
+
+`miniscope_io.vendor.opalkelly` - used for FPGA I/O
+
+#### Linux
+
+We package the OpalKelly FrontPanel SDK here, but it has an unadvertised dependency
+on some system level packages:
+
+- `liblua5.3-0`
+
+So eg. on debian/ubuntu you'll need to:
+
+```bash
+apt install liblua5.3-0
+```
+
+#### Mac
+
+No special installation should be required.
+
+#### Windows
+
+Currently windows is not implemented - see `miniscope_io/vencor/opalkelly/README.md` for
+what was done to implement Linux and Mac to see what might need to be done here, pull requests welcome :)

docs/index.md

@@ -5,12 +5,23 @@
 
 # miniscope-io
 
+```{toctree}
+:caption: Guide:
+
+guide/index
+```
+
 ```{toctree}
 :maxdepth: 2
 :caption: Contents:
 
 api/index
-changelog
+```
+
+```{toctree}
+:caption: Meta:
+
+meta/index
 ```
 
 

docs/meta/index.md

@@ -0,0 +1,8 @@
+# Meta
+
+
+```{toctree}
+changelog
+todo
+```
+

docs/meta/todo.md

@@ -0,0 +1,4 @@
+# TODO
+
+```{todolist}
+```

miniscope_io/devices/opalkelly.py

@@ -0,0 +1,55 @@
+import time
+
+from bitstring import BitArray
+
+from miniscope_io.vendor import opalkelly as ok
+
+
+class okDev(ok.okCFrontPanel):
+    """
+    I/O and configuration for an (what kind of opal kelly device?)
+
+    .. todo::
+
+        Phil: document what this thing does, including how bitfiles work
+        and how they're generated/where they're located.
+
+    """
+    def __init__(self, serial_id: str = ""):
+        super().__init__()
+        ret = self.OpenBySerial("")
+        if ret != self.NoError:
+            raise ValueError("Cannot open device: {}".format(serial_id))
+        self.info = ok.okTDeviceInfo()
+        ret = self.GetDeviceInfo(self.info)
+        if ret == self.NoError:
+            print("Connected to {}".format(self.info.productName))
+
+    def uploadBit(self, bit_file: str):
+
+        ret = self.ConfigureFPGA(bit_file)
+        if ret == self.NoError:
+            print("Succesfully uploaded {}".format(bit_file))
+        else:
+            raise ValueError("Configuration of {} failed".format(self.info.productName))
+        print(
+            "FrontPanel {} supported".format(
+                "is" if self.IsFrontPanelEnabled() else "not"
+            )
+        )
+        ret = self.ResetFPGA()
+
+    def readData(self, length: int, addr: int = 0xA0, blockSize: int = 16):
+        buf = bytearray(length)
+        ret = self.ReadFromBlockPipeOut(addr, data=buf, blockSize=blockSize)
+        if ret < 0:
+            raise ValueError("Read failed: {}".format(ret))
+        elif ret < length:
+            print("Only {} bytes read".format(ret))
+        return buf
+
+    def setWire(self, addr: int, val: int):
+        ret = self.SetWireInValue(addr, val)
+        ret = self.UpdateWireIns()
+        if ret != self.NoError:
+            raise ValueError("Wire update failed: {}".format(ret))