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added anyhow error handling in python interface
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«ratal» committed Apr 22, 2024
1 parent 9b28ef5 commit 4830a55
Showing 1 changed file with 97 additions and 78 deletions.
175 changes: 97 additions & 78 deletions src/mdfr.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@ use crate::data_holder::channel_data::ChannelData;
use crate::mdfinfo::MdfInfo;
use crate::mdfreader::MasterSignature;
use crate::mdfreader::Mdf;
use anyhow::Context;
use arrow::array::ArrayData;
use arrow::pyarrow::PyArrowType;
use arrow::util::display::{ArrayFormatter, FormatOptions};
Expand Down Expand Up @@ -47,34 +48,38 @@ impl Mdfr {
mdf.get_version()
}
/// returns channel's data, numpy array or list, depending if data type is numeric or string|bytes
fn get_channel_data(&self, channel_name: String) -> Py<PyAny> {
fn get_channel_data(&self, channel_name: String) -> PyResult<Py<PyAny>> {
let Mdfr(mdf) = self;
// default py_array value is python None
pyo3::Python::with_gil(|py| {
let data = pyo3::Python::with_gil(|py| -> PyResult<Py<PyAny>> {
let mut py_array: Py<PyAny>;
let dt = mdf.get_channel_data(&channel_name);
if let Some(data) = dt {
py_array = data.clone().into_py(py);
if let Some(m) = data.clone().validity() {
let mask: Py<PyAny> = m.iter().collect::<Vec<bool>>().into_py(py);
let locals = [("numpy", py.import("numpy").expect("could not import numpy"))]
.into_py_dict(py);
let locals = [(
"numpy",
py.import("numpy").context("could not import numpy")?,
)]
.into_py_dict(py);
locals
.set_item("py_array", &py_array)
.expect("cannot set python data");
.context("cannot set python data")?;
locals
.set_item("mask", mask)
.expect("cannot set python mask");
.context("cannot set python mask")?;
py_array = py
.eval(r#"numpy.ma.array(py_array, mask=mask)"#, None, Some(locals))
.expect("masked array creation failed")
.context("masked array creation failed")?
.into_py(py);
}
} else {
py_array = Python::None(py);
}
py_array
})
Ok(py_array)
})?;
Ok(data)
}
/// returns channel's numpy dtype
fn get_channel_dtype(&self, channel_name: String) -> Py<PyAny> {
Expand Down Expand Up @@ -125,9 +130,9 @@ impl Mdfr {
}
/// returns polar dataframe including channel
#[cfg(feature = "polars")]
fn get_polars_dataframe(&self, channel_name: String) -> Py<PyAny> {
fn get_polars_dataframe(&self, channel_name: String) -> PyResult<Py<PyAny>> {
let Mdfr(mdf) = self;
pyo3::Python::with_gil(|py| {
Python::with_gil(|py| {
let mut py_dataframe = Python::None(py);
let channel_list = mdf.mdf_info.get_channel_names_cg_set(&channel_name);
let series_dict = PyDict::new(py);
Expand All @@ -137,17 +142,17 @@ impl Mdfr {
.set_item(
channel.clone(),
rust_arrow_to_py_series(channel_data.as_ref(), channel)
.expect("Could not convert to python series"),
.context("Could not convert to python series")?,
)
.expect("could not store the serie in dict");
.context("could not store the serie in dict")?;
}
}
if !series_dict.is_empty() {
let locals = PyDict::new(py);
locals
.set_item("series", series_dict)
.expect("cannot set python series_list");
py.import("polars").expect("Could import polars");
.context("cannot set python series_list")?;
py.import("polars").context("Could import polars")?;
py.run(
r#"
import polars
Expand All @@ -156,34 +161,34 @@ df=polars.DataFrame(series)
None,
Some(locals),
)
.expect("dataframe creation failed");
.context("dataframe creation failed")?;
if let Ok(Some(df)) = locals.get_item("df") {
py_dataframe = df.into();
}
}
py_dataframe
Ok(py_dataframe)
})
}
/// returns channel's unit string
fn get_channel_unit(&self, channel_name: String) -> PyResult<Py<PyAny>> {
fn get_channel_unit(&self, channel_name: String) -> PyResult<Option<String>> {
let Mdfr(mdf) = self;
pyo3::Python::with_gil(|py| {
pyo3::Python::with_gil(|_py| {
let unit_or_error = mdf.mdf_info.get_channel_unit(&channel_name);
match unit_or_error {
Ok(unit) => Ok(unit.to_object(py)),
Ok(unit) => Ok(unit),
Err(_) => Err(PyUnicodeDecodeError::new_err(
"Invalid UTF-8 sequence in metadata",
)),
}
})
}
/// returns channel's description string
fn get_channel_desc(&self, channel_name: String) -> PyResult<Py<PyAny>> {
fn get_channel_desc(&self, channel_name: String) -> PyResult<Option<String>> {
let Mdfr(mdf) = self;
pyo3::Python::with_gil(|py| {
pyo3::Python::with_gil(|_py| {
let desc_or_error = mdf.mdf_info.get_channel_desc(&channel_name);
match desc_or_error {
Ok(desc) => Ok(desc.to_object(py)),
Ok(desc) => Ok(desc),
Err(_) => Err(PyUnicodeDecodeError::new_err(
"Invalid UTF-8 sequence in metadata",
)),
Expand All @@ -199,7 +204,7 @@ df=polars.DataFrame(series)
})
}
/// returns channel's master data, numpy array or list, depending if data type is numeric or string|bytes
fn get_channel_master_data(&mut self, channel_name: String) -> Py<PyAny> {
fn get_channel_master_data(&mut self, channel_name: String) -> PyResult<Py<PyAny>> {
// default py_array value is python None
let master = self.get_channel_master(channel_name);
self.get_channel_data(master.to_string())
Expand Down Expand Up @@ -274,7 +279,7 @@ df=polars.DataFrame(series)
let Mdfr(mdf) = self;
pyo3::Python::with_gil(|_| -> Result<(), PyErr> {
let array = array_to_rust(data)
.expect("data modification failed, could not extract numpy array");
.context("data modification failed, could not extract numpy array")?;
mdf.add_channel(
channel_name,
array,
Expand Down Expand Up @@ -445,50 +450,54 @@ df=polars.DataFrame(series)
})
}
/// plot one channel
pub fn plot(&self, channel_name: String) {
pub fn plot(&self, channel_name: String) -> PyResult<()> {
let Mdfr(mdf) = self;
pyo3::Python::with_gil(|py| {
pyo3::Python::with_gil(|py| -> PyResult<()> {
let locals = PyDict::new(py);
locals
.set_item("channel_name", &channel_name)
.expect("cannot set python channel_name");
.context("cannot set python channel_name")?;
locals
.set_item(
"channel_unit",
mdf.mdf_info.get_channel_unit(&channel_name).unwrap_or(None),
)
.expect("cannot set python channel_unit");
.context("cannot set python channel_unit")?;
if let Some(master_name) = mdf.mdf_info.get_channel_master(&channel_name) {
locals
.set_item("master_channel_name", &master_name)
.expect("cannot set python master_channel_name");
.context("cannot set python master_channel_name")?;
locals
.set_item(
"master_channel_unit",
mdf.mdf_info.get_channel_unit(&master_name).unwrap_or(None),
)
.expect("cannot set python master_channel_unit");
let data = self.get_channel_data(master_name);
.context("cannot set python master_channel_unit")?;
let data = self
.get_channel_data(master_name)
.context("failed getting master channel data")?;
locals
.set_item("master_data", data)
.expect("cannot set python master_data");
.context("cannot set python master_data")?;
} else {
locals
.set_item("master_channel_name", py.None())
.expect("cannot set python master_channel_name");
.context("cannot set python master_channel_name")?;
locals
.set_item("master_channel_unit", py.None())
.expect("cannot set python master_channel_unit");
.context("cannot set python master_channel_unit")?;
locals
.set_item("master_data", py.None())
.expect("cannot set python master_data");
.context("cannot set python master_data")?;
}
let data = self.get_channel_data(channel_name);
let data = self
.get_channel_data(channel_name)
.context("failed getting channel data")?;
locals
.set_item("channel_data", data)
.expect("cannot set python channel_data");
.context("cannot set python channel_data")?;
py.import("matplotlib")
.expect("Could not import matplotlib");
.context("Could not import matplotlib")?;
py.run(
r#"
from matplotlib import pyplot
Expand All @@ -508,15 +517,11 @@ pyplot.show()
None,
Some(locals),
)
.expect("plot python script failed");
.context("plot python script failed")?;
Ok(())
})
}
// /// export to Parquet file
// pub fn export_to_parquet(&mut self, file_name: &str, compression_option: Option<&str>) {
// let Mdfr(mdf) = self;
// mdf.export_to_parquet(file_name, compression_option)
// .expect("could not export to parquet")
// }
/// display a representation of mdfinfo object content
fn __repr__(&mut self) -> PyResult<String> {
let mut output: String;
let format_option = FormatOptions::new();
Expand All @@ -528,95 +533,109 @@ pyplot.show()
"Header :\n Author: {} Organisation:{}",
mdfinfo3.hd_block.hd_author, mdfinfo3.hd_block.hd_organization
)
.expect("cannot print author and organisation");
.context("cannot print author and organisation")?;
writeln!(
output,
"Project: {} Subject:{}",
mdfinfo3.hd_block.hd_project, mdfinfo3.hd_block.hd_subject
)
.expect("cannot print project and subject");
.context("cannot print project and subject")?;
writeln!(
output,
"Date: {:?} Time:{:?}",
mdfinfo3.hd_block.hd_date, mdfinfo3.hd_block.hd_time
)
.expect("cannot print date and time");
write!(output, "Comments: {}", mdfinfo3.hd_comment).expect("cannot print comments");
.context("cannot print date and time")?;
write!(output, "Comments: {}", mdfinfo3.hd_comment)
.context("cannot print comments")?;
for (master, list) in mdfinfo3.get_master_channel_names_set().iter() {
if let Some(master_name) = master {
writeln!(output, "\nMaster: {master_name}")
.expect("cannot print master channel name");
.context("cannot print master channel name")?;
} else {
writeln!(output, "\nWithout Master channel")
.expect("cannot print thre is no master channel");
.context("cannot print thre is no master channel")?;
}
for channel in list.iter() {
let unit = self.get_channel_unit(channel.to_string())?;
let desc = self.get_channel_desc(channel.to_string())?;
write!(output, " {channel} ").expect("cannot print channel name");
let unit = self
.get_channel_unit(channel.to_string())
.context("failed printing channel unit")?
.unwrap_or_default();
let desc = self
.get_channel_desc(channel.to_string())
.context("failed printing channel description")?
.unwrap_or_default();
write!(output, " {channel} ").context("cannot print channel name")?;
if let Some(data) = self.0.get_channel_data(channel) {
if !data.is_empty() {
let array = &data.as_ref();
let displayer = ArrayFormatter::try_new(array, &format_option)
.expect("failed creating formatter for arrow array");
.context("failed creating formatter for arrow array")?;
write!(&mut output, "{}", displayer.value(0))
.expect("failed writing first value of array");
write!(output, " ").expect("cannot print simple space character");
.context("failed writing first value of array")?;
write!(output, " ")
.context("cannot print simple space character")?;
write!(&mut output, "{}", displayer.value(data.len() - 1))
.expect("failed writing last value of array");
.context("failed writing last value of array")?;
}
writeln!(
output,
" {unit} {desc} "
).expect("cannot print channel unit and description with first and last item");
" {} {} ",unit, desc
).context("cannot print channel unit and description with first and last item")?;
} else {
writeln!(output, " {unit} {desc} ")
.expect("cannot print channel unit and description");
writeln!(output, " {} {} ", unit, desc)
.context("cannot print channel unit and description")?;
}
}
}
output.push_str("\n ");
}
MdfInfo::V4(mdfinfo4) => {
output = format!("Version : {}\n", mdfinfo4.id_block.id_ver);
writeln!(output, "{}", mdfinfo4.hd_block).expect("cannot print header block");
writeln!(output, "{}", mdfinfo4.hd_block).context("cannot print header block")?;
let comments = &mdfinfo4
.sharable
.get_comments(mdfinfo4.hd_block.hd_md_comment);
for c in comments.iter() {
writeln!(output, "{} {}", c.0, c.1).expect("cannot print header comments");
writeln!(output, "{} {}", c.0, c.1).context("cannot print header comments")?;
}
for (master, list) in mdfinfo4.get_master_channel_names_set().iter() {
if let Some(master_name) = master {
writeln!(output, "\nMaster: {master_name}")
.expect("cannot print master channel name");
.context("cannot print master channel name")?;
} else {
writeln!(output, "\nWithout Master channel")
.expect("cannot print thre is no master channel");
.context("cannot print thre is no master channel")?;
}
for channel in list.iter() {
let unit = self.get_channel_unit(channel.to_string())?;
let desc = self.get_channel_desc(channel.to_string())?;
write!(output, " {channel} ").expect("cannot print channel name");
let unit = self
.get_channel_unit(channel.to_string())
.context("failed printing channel unit")?
.unwrap_or_default();
let desc = self
.get_channel_desc(channel.to_string())
.context("failed printing channel description")?
.unwrap_or_default();
write!(output, " {channel} ").context("cannot print channel name")?;
if let Some(data) = self.0.get_channel_data(channel) {
if !data.is_empty() {
let array = &data.as_ref();
let displayer = ArrayFormatter::try_new(array, &format_option)
.expect("failed creating formatter for arrow array");
.context("failed creating formatter for arrow array")?;
write!(&mut output, "{}", displayer.value(0))
.expect("cannot print channel data");
.context("cannot print channel data")?;
write!(output, " .. ")
.expect("cannot print simple space character");
.context("cannot print simple space character")?;
write!(&mut output, "{}", displayer.value(data.len() - 1))
.expect("cannot channel data");
.context("cannot channel data")?;
}
writeln!(
output,
" {unit} {desc} "
).expect("cannot print channel unit and description with first and last item");
" {} {} ",unit, desc
).context("cannot print channel unit and description with first and last item")?;
} else {
writeln!(output, " {unit} {desc} ")
.expect("cannot print channel unit and description");
writeln!(output, " {} {} ", unit, desc)
.context("cannot print channel unit and description")?;
}
}
}
Expand Down

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